I can understand your hesitation to re-rip but having just finished ripping 2600 CD's to FLAC I am finally happy. With drive space so cheap I think it's worth going to lossless now more than ever. Once your collection is in a lossless format you can pretty much convert to any future format without loosing any audio information. I havent pulled a CD out in weeks.
I was originally at all 320kbps MP3 and was pretty happy but I have to admit some of the stuff is considerable better ripped to FLAC.
I would re-rip the entire collection and be done with it ... I also put together an Excel spreadsheet while I was ripping to inventory all my CDs. It seemed at first like a long and daunting task but it was kinda fun. I pulled out stuff I hadnt heard in a while and drank a few beers while listening to music and swapping CDs. It was kind of a Friday Night activity for a while. One thing to watch is errors on the disc. I am now using DB Poweramp which is really good with error recovery. I noticed the first time I ripped to MP3 even though the program said the disc ripped fine
I had a few errors. Im not sure what Apple has for ripping programs but I would dig deep in the settings and see if there is a secure mode while ripping the CDs. It generally takes longer to rip but you dont want to have to go back and do it twice. Lastly Spend the $100/200 and get a second (or third and fourth) USB/Firewire external drive for backup. I have 2 Terabytes of drive space that sit unplugged on a shelf, with the whole collection backed up just in case.
