Got it working, and have done a trial run by synching some of the converted tracks to my ipod and back again after playing them. The Flac files had updated their playcounts. And there seems to be no loss on my ipod with regard to album art, lyrics etc.
And it's turning out to be a lot more straightforward than I thought. My synch playlist just points to the path for the converted files, and that seems to be it.
I haven't tried it with my various shuffle playlists (worked by ratings, last played etc.) yet, but I think if I just exclude the Flac files from those it should work fine.
And yes, converting all those albums is a bit of a pain, but once off pain I can deal with. It was the constant reconverting I found arduous. You have given me months of my life back.

Kudos!