Is there a command I can add to the .bat file which will make it NOT close the window after it's done copying so I can sort through whichever ones aren't copying over (because they're missing), then manually try to find those?
pause. This waits for a keypress, after that the window is closed.
You can also direct the output into a .txt file which makes finding the missing files more comfortable.
Open the .bat file with a text editor. It should look something like this
md _vertshmups
copy 1942.zip _vertshmups
::copy 1943.zip _vertshmups
copy 1943u.zip _vertshmups
copy 19xx.zip _vertshmups
copy aerofgts.zip _vertshmups
copy vspsx.zip _vertshmups
copy agalletu.zip _vertshmups
::copy agallet.zip _vertshmups
copy batrideru.zip _vertshmups
::copy batrider.zip _vertshmups
copy batsugunsp.zip _vertshmups
::copy batsugun.zip _vertshmups
Now go into the search and replace menu, choose replace and replace
.zip _vertshmups
with
.zip _vertshmups >>error.txt
Save and start the .bat file. When it's done, you will have an error.txt file in the destination directory (that would be _vertshmups in my example). Open error.txt in a text editor, look at the first error message, copy some of the text and use the search function to hop from error to error.