I dispute this claim. The underlying artifact format for Fossil is compatible
back to the beginning. There have been enhancements, but nothing that would break. And there have been no reports of breakage among the countless users on the Fossil Forum.
I suspect what the OP encountered was that he checked in some things using a newer version of Fossil that had enhanced capabilities. (For example, Fossil originally only use SHA1 hashes, but was enhanced to support both SHA1 or SHA3 after the SHAttered attack.) Then the OP tried to extract using an older Fossil that didn't understand the new feature and returned an error. I'm guessing at this, of course, but that seems like the most likely scenario.
I have never once made a backup of SQLite repo or the Fossil self-hosting repo, or any of the other 100+ Fossil repositories that I have at hand. I've cloned the repos to other machines as disaster protection. In fact, I have cron jobs running on machines all over the world that "sync" critical Fossil repositories (such as SQLite) once an hour or so. But I have never even once made a pure backup.
I did have the primary SQLite repo go corrupt on my once, years ago. Somehow, file descriptor 2 got closed. Then when the SQLite database that is the repository was opened, it opened on file descriptor 2. Then some bug in Fossil caused an assert() to fire which wrote on file descriptor 2, overwriting part of the database. I restored the repo from a clone, fixed the assertion fault in Fossil, and enhanced SQLite so that it refuses to use a file descriptor less than 3.
I suspect what the OP encountered was that he checked in some things using a newer version of Fossil that had enhanced capabilities. (For example, Fossil originally only use SHA1 hashes, but was enhanced to support both SHA1 or SHA3 after the SHAttered attack.) Then the OP tried to extract using an older Fossil that didn't understand the new feature and returned an error. I'm guessing at this, of course, but that seems like the most likely scenario.
I have never once made a backup of SQLite repo or the Fossil self-hosting repo, or any of the other 100+ Fossil repositories that I have at hand. I've cloned the repos to other machines as disaster protection. In fact, I have cron jobs running on machines all over the world that "sync" critical Fossil repositories (such as SQLite) once an hour or so. But I have never even once made a pure backup.
I did have the primary SQLite repo go corrupt on my once, years ago. Somehow, file descriptor 2 got closed. Then when the SQLite database that is the repository was opened, it opened on file descriptor 2. Then some bug in Fossil caused an assert() to fire which wrote on file descriptor 2, overwriting part of the database. I restored the repo from a clone, fixed the assertion fault in Fossil, and enhanced SQLite so that it refuses to use a file descriptor less than 3.
See also: https://fossil-scm.org/home/doc/trunk/www/selfcheck.wiki