The generated Hash-file isn't structured correctly, this in turn means that FileBot can't find the hashed files when loaded back in.
Below I've shown what the problem is and how it should be fixed.
I've already tested this by editing the file in a text-editor and loading it back into FileBot, after this change (dash changed to underscore) FileBot has no trouble finding the files again.
Is structured as:"HashCode" ?SHA3-384*"FileName"
Should be structured as: "HashCode" ?SHA3_384*"FileName"
BugReport + Fix: SHA3 file not structured correctly
Re: BugReport + Fix: SHA3 file not structured correctly
Good catch! Fixed with FileBot r8373.