A solution to your issue would be to use your procmailrc file to save a copy of the mail to a Maildir format.
Maildir keeps each mail as a separate file, which solves your one problem. Additionally, if you copy the mail it will still go the the other existing locations:
your procmailrc would have the following (or similar lines) near the top:
:0c: $HOME/Maildir/
You would need to create the folder Maildir
in your home directory still.