I did the exact same thing about 8-9 years ago where I converted all my FLAC to ALAC for compatibility with IOS. I totally agree with the other posts here if you don't need to use iTunes I wouldn't do it...(I used dBpoweramp at the time but I do this conversion all the time with MC21 for single albums and it works like a charm...) And I don't really see the point of having lossless files on my Ipod or Iphone...Unless connected to an external DAC but I totally understand why others may want it...
And one other thing to keep in mind, ALAC files are usually 10-15% larger than FLAC so will take up more space.
Aside from this, I don't have any other issues with ALAC files vs FLAC in JRiver (except that minor issue I reported about changing capitalization.) and my tags are complete and well organised.
One thing I still do outside of JRiver is to tag itunnorm with either dBpoweramp or MP3 tag (That is optional and can be done by iTunes and JRiver will do it anyway when you sync your IOS device) I would like that feature in JRiver
AND I use MC21 to sync my Ipod Classic 5th Gen it works like a charm using MP3 extreme...
So If I had to do this allover again here is how I would do it today:
1. Make a mirror backup of all my FLAC files on a separate hard drive out of the monitored folder by MC. (Assuming they are all in the same folder that's how I have them...)
2. Backup my MC library and save it on that same hard drive. (Using File -> Library -> Backup Library...)
3. Configure the conversion as per snapshot attached.
4. Try it first on a few albums and see how it goes
5. Then cross my fingers and run the whole folder!!
6. Check for any duplicate files or flac remnants either with MC or windows explorer. (In the past doing this would sometimes leave the FLAC original file but the ALAC was created just fine without errors)
If this fails you can just delete the new folder, bring back your backup folder and restore the previous library...
Good Luck AND please do this at your own risk I obviously haven't tested this and I'm not planning to!!!