Why do you need lossless files for your oldest PC? Are you accessing the files through a network share? (I suppose you already know that MC's Media Server and MJ are not compatible.) Could you just convert the APE files to a high quality compressed format for that PC? E.g. to MP3 with a custom setting "--alt-preset standard". In my opinion that makes almost transparent files, which are good enough for most listening purposes. Though not for transcoding, but you still have your APEs.
If you really need to replace the 3.99 APEs with 3.97 APEs and you like to keep your current MC library information, I think you could do this:
1. Backup everything: the files and MC Library. (A good practice anyway)
2. Convert the 3.99 APEs to wave (With MC or Monkey's Audio 3.99).
3. Convert the waves to Monkey's Audio 3.97 (
http://www.monkeysaudio.com/files/MAC_397F.exe)
4. Now your new 3.97 APEs have original filenames but no tags. Replace your original 3.99 files with the 3.97 versions (outside MC). Let MC write the tags: Library Tools -> Update tags (from library).
Make some test runs before converting all files.
This was for you already ripped 3.99 APE files. I would use EAC and MA 3.97 for new rips and import them to MC and MJ afterwards.
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Topic: Ripped APEs with MC...now can't import into MJ (Read 2386 times)