Why didn't they stay in their playlists?

I looked at the size of my library - huge! It's huge becuase I ripped all my CD's to iTunes as aiff to maintain quality a while back, but now I figured it was time to convert to Apple Lossless. I went to the iTunes music folder, filtered by bitrate to select out all the 1411 Kb aiff files, selected all of them, and right clicked to convert to Apple Lossless. The process went smoothly enough, but when I checked, the conversion had stripped all the playlist assignments for every tune. I had a bunch of empty playlists, and a huge list in "recent imports", all piled in to this single huge file.

I shouldn't have to go back and re-assign every tune to it's previous playlists just because I wanted to convert format. There must be a workaround that leaves them with the playlist designations before they were converted. Can anybody offer any help? Presently, I am just letting time machine rebuild the old files.