Short answer: Yes, and actually it was from 1945 until 1991, with the implementation of the so-called Two Plus Four Agreement, which was signed the previous year.

Before going any further, it's probably best to define sovereignty. According to Merriam-Webster, the most relevant definitions are:

2
a : supreme power especially over a body politic
b : freedom from external control : autonomy
c : controlling influence
3
: one that is sovereign; especially : an autonomous state

So, in short, in order for a state to be sovereign, it must exert final control over it's peoples and territory. When the Germans surrendered, they explicitly gave up this control.

As one can see from the German instruments of surrender, signed on [May 7th](https://en.wikisource.org/wiki/German_Instrument_of_Surrender_(7_May_1945)) and [May 8th](https://en.wikisource.org/wiki/German_Instrument_of_Surrender_(8_May_1945)) (the Soviet General Zhukov was not present at Rheims, on May 7, so the Soviets forced the Germans to sign a second surrender instrument), the Germans explicitly

surrender[ed] unconditionally to the Supreme Commander, Allied Expeditionary Force and simultaneously to the Soviet High Command all forces on land, sea, and in the air who are at this date under German control.

It should be noted, however, that these declarations only technically covered military forces, and were signed under the orders of the so-called Flensburg government (headed by Doenitz), which the Allies did not recognize as a legal government (and in fact arrested the leaders of said government upon catching up with them). To make up for this legal hole, the four allied powers issued jointly the [Berlin Declaration](https://en.wikisource.org/wiki/Berlin_Declaration_(1945)) on June 5, 1945, which declared by fiat that which had been already effectively accomplished through battle - the assumption of complete control by the Allies of the German nation:

The German armed forces on land, at sea and in the air have been completely defeated and have surrendered unconditionally and Germany, which bears responsibility for the war, is no longer capable of resisting the will of the victorious Powers. The unconditional surrender of Germany has thereby been effected, and Germany has become subject to such requirements as may now or hereafter be imposed upon her.

There is no central Government or authority in Germany capable of accepting responsibility for the maintenance of order, the administration of the country and compliance with the requirements of the victorious Powers.

It is in these circumstances necessary, without prejudice to any subsequent decisions that may be taken respecting Germany, to make provision for the cessation of any further hostilities on the part of the German armed forces, for the maintenance of order in Germany and for the administration of the country, and to announce the immediate requirements with which Germany must comply.

The Representatives of the Supreme Commands of the United States of America, the Union of Soviet Socialist Republics, the United Kingdom and the French Republic, hereinafter called the "Allied Representatives," acting by authority of their respective Governments and in the interests of the United Nations, accordingly make the following Declaration:

The Governments of the United States of America, the Union of Soviet Socialist Republics and the United Kingdom, and the Provisional Government of the French Republic, hereby assume supreme authority with respect to Germany, including all the powers possessed by the German Government, the High Command and any state, municipal, or local government or authority. The assumption, for the purposes stated above, of the said authority and powers does not affect the annexation of Germany.

The Governments of the United States of America, the Union of Soviet Socialist Republics and the United Kingdom, and the Provisional Government of the French Republic, will hereafter determine the boundaries of Germany or any part thereof and the status of Germany or of any area at present being part of German territory.

...

ARTICLE 13

(a) In the exercise of the supreme authority with respect to Germany assumed by the Governments of the United States of America, the Union of Soviet Socialist Republics and the United Kingdom, and the Provisional Government of the French Republic, the four Allied Governments will take such steps, including the complete disarmament and demilitarization of Germany, as they deem requisite for future peace and security.

(b) The Allied Representatives will impose on Germany additional political, administrative, economic, financial, military and other requirements arising from the complete defeat of Germany. The Allied Representatives, or persons or agencies duly designated to act on their authority, will issue proclamations, orders, ordinances and instructions for the purpose of laying down such additional requirements, and of giving effect to the other provisions of this Declaration. All German authorities and the German people shall carry out unconditionally the requirements of the Allied Representatives, and shall fully comply with all such proclamations, orders, ordinances and instructions.

---

Although the creation of the Federal Republic of Germany (BRD/West Germany) and the German Democratic Republic (DDR/East Germany) returned much control to Germans themselves (obviously more for the Federal Republic than for the German Democratic Republic), neither state was fully sovereign until 1991. In the Treaty on the Final Settlement With Respect to Germany, usually called the Two Plus Four Agreement, Article 7 reads:

ARTICLE 7

(1) The French Republic, the Union of Soviet Socialist Republics, the United Kingdom of Great Britain and Northern Ireland and the United States of America hereby terminate their rights and responsibilities relating to Berlin and to Germany as a whole. As a result, the corresponding, related quadripartite agreements, decisions and practices are terminated and all related Four Power institutions are dissolved.

(2) The United Germany shall have accordingly full sovereignty over its internal and external affairs.

The treaty, signed in Sept 1990, went into effect on March 15, 1991. In the interim, on Oct. 3, 1990, the Day of German Unity, the two German states legally merged, with the Federal Republic effectively absorbing the former German Democratic Republic into its territory.

---

Regarding your question about whether there were Germans who feared that their post-war status might be indefinite, I'm sure there were, especially in the DDR, but I don't have any particular person or group in mind that I can point to or sources that explicitly point to such, and to be frank, don't really want to look them up. So I'll leave that to someone else.

Finally, I should note that there are some folks, especially in Germany, who will argue that because the German armed forces are fully integrated into the NATO command structure, that they do not remain fully sovereign to this day, that's legally incorrect. It's my understanding that the German government, should it wish it, could remove its forces from NATO command with a simple majority vote of the Bundestag, but I'll let an expert on present German politics clarify that if it comes up further.

Edit: links fixed. Still caught in spam filter?

Ok, please know that this is an incredibly complex question due to the legal situation of the Allied occupation in German and that there are still contesting legal theories about this subject within the German community of legal scholars.

The majority opinion of German legal scholars that ultimately found entrance in the 2+4 treaty of 1991 is that while Germany temporarily ceded sovereignty, it did not cease to exist as a sovereign entity between 45 and 49. Now, if you are like me reading this the first time, you are probably thinking "WTF? What's the difference?" right now.

Well, let me explain (I am not legal scholar, so forgive me for skipping over some of the finer points of this): It is the majority opinion of German legal scholars the the German Federal Republic is the successor state to the German Reich within its borders of 1937. According to this view the German Reich within the borders of 1937 transformed into its successor state, the German Federal Republic, when the constituents of the Reich, its sovereign federal states, i.e. Hamburg, Schleswig etc., signed the German Grundgesetz in 1949.

In this view, in the time between 45 and 49, German ceded sovereignty to the Allied occupational authority but did not cede to exist as a sovereign entity of international law. This view was shared by the Allies to some extent since they made it a clear point through for example the Berlin declaration of June 1945 that the Allies despite exercising governmental control did not want to annex Germany and granted that all international treaties signed by the German Reich within the borders of 1937 were still in effect (e.g. the concordat the German Reich had signed with the Vatican in the 30s). This idea was further compounded by the re-establishment of the federal states in Germany in July 1945, which legal existed as sovereign constituent nations of the German Reich within the borders of 1937 by virtue of having to fulfill the treaties signed by said Reich.

In essence, the idea was that German Reich as a state continued to exist as a sovereign entity but in a sort of limbo in that it was unable to exercise its sovereignty because it had been temporarily seized by the Allies. This view was important further down the road with the Hallstein Doctrine of the Federal Republic that said, it was the only German state and the GDR did not exist and everyone who had relations with the GDR could not have relations with the FRG. It also was important for the 2+4 treaty because this view is the basis for the federal states of the GDR joining the FRG by signing the Grundgesetz.

As for the fear of an indefinite occupation: The preparations for a new German state began in essence in 1946 when the Allied military administration charged the federal states resp. the political parties of Germany with developing a new state framework for a new overall state. So while some might have feared that occupation might last longer than 49, there certainly was a sense that at some point Germany would regain control over its government.

Edit: One additional note. It was the 2+4 treaty which returned full sovereignty to the German government but seeing as to how the Federal Republic and GDR had been able to for example sign international treaties before they existed as sovereign entities within international law.

Sources: My sources for this are mainly German texts and I don't know how of how much interest they are for you. If anybody is interested, I am happy to provide, please ask.