SubGit itself is designed to be case-sensitive and thus differentiate cases internally and does not remove any branches because of that. But if SubGit writes the data to a case-insensitive filesystem, then the file may indeed be overwritten; that may happen on Windows, for example, since NTFS is case-insensitive by default, could it be the case?
It’s not clear why the import fails at 99%, and I’m afraid that it’s hard to make any conclusions without additional information. Could you please advise what the error does SubGit show when fails? Are there any exceptions in the SubGit import logs?
You were totally right. I spun up a linux vm and run the conversion again and this time everything was fine. You were spot on with NTFS being the problem.