The "chupatty movement" that you refer to was a very strange story, and one I covered in detail in an essay a couple of years ago. Since this addresses your main query, I am pasting it below, but the short answer to your question is that it is still quite mysterious exactly what the chapatis symbolised and why they were circulated – even the people carrying them did not know the reasons why. It's more likely than not that they had nothing at all to do with the rebellion that subsequently broke out.

More below....

“There is a most mysterious affair going on throughout the whole of India at present,” wrote Dr Gilbert Hadow in a letter to his sister at home in Britain dated March 1857. “No one seems to know the meaning of it… It is not known where it originated, by whom or for what purpose, whether it is supposed to be connected to any religious ceremony or whether it has to do with some secret society. The Indian papers are full of surmises as to what it means. It is called ‘the chupatty movement.’” [Hibbert p.59]

The “movement” that Dr Hadow was describing was a remarkable example of rumour gone wild. It consisted of the distribution of many thousands of chapatis – unleavened Indian breads – which were passed from hand to hand and from village to village throughout the mofussil (interior) of the Subcontinent. That these chapatis really existed is beyond doubt; what made their distribution truly bizarre and inexplicable was that nobody knew for sure what they were for. Most Indians thought they were the work of the British, who – through the medium of the East India Company – had ruled over large portions of the country for almost exactly a century (and were, according to one well-known prophecy, due to be unseated at that century’s end). The British, who at least knew that they had nothing to do with the mysterious transmission, guessed they were a piece of mischief-making on the part of the Indians, though opinion was divided as to whether the breads came from the east, near Calcutta (Kolkata), from the north, in the province of Oude (Avadh), or from Indore, in centre of the country. Extensive enquiries into the meaning of the breads produced plenty of theories but few firm facts; even the runners and watchmen who baked them and actually carried them from village to village “did not know why they had to run through the night with chupatties in their turbans,” although they took them just the same [Hibbert p.60].

The chupatty movement first came to British attention early in February 1857. One of the first officials to encounter it was Mark Thornhill, who was the magistrate in the little Indian town of Mathura, near Agra. Thornhill came into his office one morning to find four “dirty little cakes of the coarsest flour, about the size and thickness of a biscuit” lying on his desk. These had – he was informed – been brought in by one of his Indian policemen, who had received them from a puzzled village chowkidar(watchman). And where had the chowkidar got them? “A man had come out of the jungle with them, and given them to the watchman with instructions to make four like them and to take these to the watchman in the next village, who was to be told to do the same.” [Thornhill p.2]

Thornhill carefully examined the chapatis in his office. There was nothing at all unusual about them. They bore no message, and were identical to the breads cooked in every home in India, which formed (and still form) a staple part of the locals’ diet. Yet the magistrate’s discreet enquiries soon revealed that many hundreds of chapatis were passing through his district, and through other parts of India as well – everywhere from the Narmada river in the south to the border with Nepal several hundred miles to the north. The breads formed, in short, what amounted to a culinary chain letter, and it was one that was spreading with such spectacular rapidity that Thornhill’s boss George Harvey, in Agra, calculated that a wave of chapatis was advancing across his province at the rate of somewhere between 100 and 200 miles a night. [Wagner p.63]

This discovery was particularly disconcerting, since the chapatis were moving vastly more swiftly than the fastest British mails could manage, and urgent enquiries were made as to the source and the meaning of the “movement”. This yielded the information that the distribution of breads was far more widespread than anyone in Agra had yet realised, and that the Indians who received them generally took them as some sort of a sign. Beyond that, however, opinions remained divided.

From the North-West Provinces:

I have the honour to inform you that a signal has passed through numbers of the villages in this district, the purport of which has not yet transpired…A Chowkeydar, on receiving one of these cakes, has had five or six more prepared, and thus they have passed from village to village… An idea has been industriously circulated that the Government has given the order.

[W. Ford, magistrate, Goorgaon, to Simon Fraser, Commissioner, Delhi, in Kaye p.632]

From Delhi:

I did hear of the circumstance. Some people said that it was a propitiatory observance to avert some impending calamity; others, that they were circulated by the Government to signify that the population throughout the country would be compelled to use the same food as the Christians, and thus be deprived of their religion; while others again said that the chupatties were circulated to make it known that Government was determined to force Christianity on the country by interfering with their food, and intimation of it was thus given that they might be prepared to resist the attempt.

Q. Is the sending of such articles about the country a custom among the Hindoos or Mussulmans; and would the meaning be at once understood without any accompanying explanation?

A. No, it is not by any means a custom; I am 50 years old, and never heard of such a thing before.

[Evidence of Jat Mall, news-writer [summariser of court news] to the Lieutenant Governor of Agra, “Trial of the King of Delhi,” Parliamentary Papers, 1859, 1st Session p.74]

From Nimach, near Bombay:

At the time they appeared in Nimar, they were everywhere brought from the direction of Indore. That city was at the time afflicted with a severe visitation of cholera, and numbers of the inhabitants died daily. It was at the time understood by the people of Nimar, and is still believed, that the cakes of wheat were dispatched from Indore after the performance over them of incantations that would ensure the pestilence accompanying them. The cakes did not come straight from North to South, for they were received at Bujenggbur, more than half-way between Indore and Gwalior, on the 9th of February, but had been distributed at Mundlaiser on the 12th of January.

[Richard Harte Keatinge, VC, in Kaye pp.572-3]

From Delhi:

It was alluded to [in the native newspapers], and it was supposed to portend some coming disturbance, and was, moreover, understood as implying an invitation to the whole population of the country to unite for some secret objective afterwards to be disclosed.

[Evidence of Chuni Lal, news-writer,  “Trial of the King of Delhi,” Parliamentary Papers, 1859, 1st Session pp.83-4.]

From Oude:

Some time in February 1857, a curious occurrence took place. A Chowkeydar ran up to another village with two chupatties. He ordered his fellow-official to make ten more, and give two to each of the five nearest village Chowkeydars with the same instructions. In a few hours the whole country was in a stir, from Chowkeydars flying around with these cakes. The  signal spread in all directions with wonderful celerity. The magistrates tried to stop it, but, in spite of all they could do, it passed along to the borders of the Punjab. There is reason to believe that this was originated by some intriguers of the old Court of Lucknow.

[Ireland p.23]

From Delhi:

Nobody can tell what was the object of the distribution of the chupatties. It is not known who first projected the plan. All the people in the palace wondered what it could mean. I had no conversation with the King on the subject; but others talked in his presence about it, wondering what could be the object.

[Statement of Hakin Ahsan Ullah, confidential physician to the King of Delhi, in Kaye p.636]