Is your goal to sync/mirror two directories or to get the differences between them (because you mention a list of files being absent, which you'd like to copy finally -> which sounds like a sync again though o).
To quickly sync two directories with a press of a buttin I use robocopy.exe (it comes with windows).
@leavedoswindowopen
Confirm MSG="Synchronize (mirror to destination) with Robocopy?\n\nfrom:\n{sourcepath$} \n\nto:\n{destpath$} " TITLE=Robocopy.exe
Robocopy.exe {sourcepath$} {destpath$} /V /E /NP /R:0 /W:0 /COPYALL /PURGE /DCOPY:T
You need the "Confirm" script addin for the confirmation dialog (or remove the line if you want to go without it):
https://www.haage-partner.de/forum/viewtopic.php?f=45&t=4926
You can also check out the CompareEx script addin:
https://www.haage-partner.de/forum/viewtopic.php?f=45&t=4956
It allows you to compare two tabs (in flatview as well). I have an updated version which is more flexible and not uploaded yet anywhere, but you might find the version I linked to to be sufficient to find out whether this would help you.
Saving the names and paths of missing/absent files into file/clipboard can be done with SelectEx, another script addin: