Dependencies/Collect files problems

in 26,2,1 version Depencies/Collect files is working differently from older versions and it’s working WRONG…
I have folders with names 001, 002, 003, 004 and inside are sub folders with rendered images.
However when I do Collect files, all the folders are “flatened” and all image sequences are put in single folders with changed names, but not all folders are processed and half of the sequences are gone or replaced with wrong ones….