Problem is specific to Win64 version it seems
Reproduced on 300+ region files:
ChunkCleaner-Win64.exe -path server_0303/region -newPath server_0303/unused/0 -minInhabitedTicks 10000
The same happens with delete mode
Rerunning the tool results in moving\deleting another batch of 2-5 files
OS Windows 10 Pro 22H2