Ok so after reading the possible solution I had to have a go with it right now.
The first code you posted BC_Programmer has allowed me to do exactly what I wanted. I have tweaked it a little to search for a specific file determined when the batch is run, because there are multiple files that exist on both A: and E: that are never changed and so would never need copying. Also, the /y was giving me an invalid switch error (maybe because of the changes I made?). I think this is something to do with a confirmation prompt(?), but I removed it and it worked without the need to confirm overwrite.
The code I used:
copydirs.bat
for %%F in (%1.abc) do checkflp.bat %%F
checkflp.bat
for %%D in (A N) do if exist A:\%%D\%1 copy %1 A:\%%D\%1
Many thanks again for your kind help.