I've taken a look at the books I have available on the Brest-Litovsk treaty, and I can't see mention of any discussion or negotiation over the status of the Baltic Fleet. This probably wasn't brought up for a number of reasons.
The first of these was that after Jutland, the Germans had abandoned their policy of seeking a decisive battle with the British. Even with the Baltic Fleet, the Germans still couldn't hope to match British numbers in the North Sea. While the Battle of Jutland had been a numerical loss for the British, they could still afford to lose another ten battleships before the numbers were equal. While the seven battleships, nine cruisers and 59 destroyers of the Baltic Fleet could go some way towards evening this balance, the German navy would still have been the underdog. Perhaps if the opportunity to obtain eight dreadnoughts had appeared earlier in the war, Germany might have taken it, but by 1918 they had stopped making serious attempts to break the British fleet.
The second reason is one of pure practicality. The Baltic fleet was frozen in to its anchorages at Helsingfors and Kronstadt from January-April, and so it would have taken at least a month before the ships could actually set sail. Additionally, the Germans would have needed to find a large amount of additional sailors to be able to crew the ships properly. See below a list of the ships which the Germans could have seized, and their crew size:
| Ship Name | Type | Complement |
|---|---|---|
| Gangut, Petropavlovsk, Poltava, Sevastopol | Dreadnought | 1149 |
| Andrei Pervozvanny, Imperator Pavel I | Pre-Dreadnought | 956 |
| Rurik | Armoured Cruiser | 899 |
| Gromoboi | Armoured Cruiser | 874 |
| Rossia | Armoured Cruiser | 839 |
| Tsesarevich | Pre-Dreadnought | 779 |
| Aurora | Light Cruiser | 590 |
| Bogatyr | Light Cruiser | 581 |
| Oleg | Light Cruiser | 576 |
| Admiral Makarov, Bayan | Armoured Cruiser | 568 |
| Diana | Light Cruiser | 540 |
| 59 destroyers | Destroyer | 70-100 |
| Total | 16,326 |
Finding 16,326 additional skilled sailors after four years of hard war and combined naval losses would have been a tall order for the German Navy. Getting those additional crews used to unfamiliar weapons, engines and communication systems in time for a decisive battle would have been very difficult, as would finding ammunition for the Russian guns. While the majority of the Baltic fleet were modern, 20th Century ships, finding the manpower and training the crews to the required standard would have been very difficult at that point in the war.
The third reason is that the Bolshevik Government were dependent on the manpower and support of the Baltic Fleet sailors at Kronstadt during the Civil War. The Kronstadt sailors had proven loyal allies to the Bolsheviks, and had provided armed support during the October Revolution. If the Bolsheviks had appeared willing to simply hand over the fleet to the Germans, it's likely that their support from the sailors would have disappeared when they needed it most. The light cruiser Aurora had played a key role during the October Revolution and storming of the Winter Palace, and handing over a symbol of the revolution would have been a serious affront. It's highly likely that had the Germans asked for the fleet, they would have been refused.
In conclusion, the Germans didn't plan on attacking the British any time soon; had they obtained the ships, they wouldn't have had enough men or time to make the ships battle ready; and had they demanded them, the Bolsheviks would most likely have refused.
Sources:
Evan Mawdsley, 'The Baltic Fleet and the Kronstadt Mutiny' Soviet Studies, Vol. 24, No. 4 (Apr., 1973), pp. 506-521
Evan Mawdsley, The Russian Revolution and the Baltic Fleet: War and Politics February 1917 - April 1918 (1978).