You should be able to use my version of Tag to export the cue sheet of an .ape or .flac (if it is just using a CUESHEET tag) file.
You would use one of the following:
--tocue <scheme> : output cuesheet tag to file, name generated from <scheme>
--tocuen <name> : output cuesheet tag to file <name>
--tocuea : output cuesheet tag to file, name generated from source
E.g.:
TAG.EXE --tocuea myfile.ape
... should result in myfile.ape.cue (or myfile.cue, I can't remember!) in the source folder.
Used in conjunction with FOR /R you could process all files in a folder and its subfolders.
NB: This assumes that you've used a tag called "CUESHEET". If you haven't you could try:
--tostdoutn <tag> : write <tag> value to stdout
E.g.:
TAG.EXE --tostdoutn CUE --hideinfo --hidetags --hidenames myfile.ape>myfile.ape.cue
This thread may be of some further use (I knew I'd written out an tostdoutn example before, at least once).
I can't remember whether CueProc or ACDIR would help in this situation, I think they will just use embedded cue sheets to pass to an encoder, but I'm not sure.