Modifications made by BlackFireBR's tools are simply unsupported, the patching method he used doesn't work anymore (ever since I released my library, it's why I did it), and they're not tracked by my tools as my tools use a different format to "log" modifications, BlackFireBR's log was done into a separate file.
Since those modifications are not supported, they're (usually, some might be) not recognized to begin with, so a "clean" meta might actually be a modded meta, hence the crash at startup, which is caused by meta corruption. As for why there isn't a clean backup created by BlackFireBR's tools, the way his tools used to create backups was by checking the size of the meta file and comparing it to the previous backup, there are a few issues with this:
1. If an update doesn't change the meta file size (it can happen), a new backup will not be created, since the tools never checked for the version number inside the meta file, it would detect there's a new version, so when you restore "backup", you might be restoring an older meta file.
2. Since my library logs modifications at the end of the meta file, the file size increases, this causes the old tools to create a "backup" of an already modded meta.
BlackFireBR updated his tools to no longer modify the meta file and to not create new backups, instead that process is handled by my library and tools due to improved support, optimizations, and a different patching method that remains compatible for textures.
There's a reason why you're asked to check that all the tools are up to date before querying for help, you're also asked for certain details, but no one bothers to read the guidance anyway...