Thanks Brad. We have just released a
new BETA version v3.0.26, can you please try again?
I wasn't able to recreate the issue directly, but v3.0.25 had a bug with how files were tracked and I think this was the problem.
I also find Resynchronize / Reload a bit confusing. The reload function is if you close a file because you don't need it and later decide you do. In this case you want to reapply the directory monitor without making any other changes to any of the other files. Importantly, you don't want to remove log entries for a file which has been rolled because the target file no longer contains the log entries you may need.
Alternatively, I could close a file and Reload the monitor to mirror the file system, but only for that specific file. Other files could still show the rolled entries.
Resynchronize is more extreme. Everything gets closed and reopened such that when the operation completes all files will mirror the source files.
I think both commands serve a purpose, but I would like to make the intention more clear. Maybe "Hard Reload" / "Soft Reload" would be better? I have renamed the commands in the latest BETA.

In summary:
Soft Reload = Reopen closed files.
Hard Reload = Close and reopen everything.