I can tell you what I do or have done replacing lossy with lossless. It uses the Additional Tagging Tools plug-in.
1. Tag the replacement files as close to the originals as possible. I use mp3tag and picard because most of my files were tagged this way I usually get the same results as before.
2. Import lossless files to the inbox
3. Right-click one, search->Find album
4. Sort the resulting list, which should be both versions and in tracks view, so each version is together in the proper order. For me and the way I tag my files, this is by the "Path" field.
5. Select the old files, rescan just in case (I've got a keyboard shortcut for this for efficiency).
6. In ATT, Copy tags to clipboard and select all of the relevant ones that are important to you (I've got a keyboard shortcut for this for efficiency)
7. Select the new version (again, must be in the same order) and paste these tags from ATT (I've got a keyboard shortcut for this for efficiency)
8. Open one of the original files and copy the artwork (if I haven't downloaded a better version with the better version of the audio)
9. Paste the artwork into the new versions (if I haven't downloaded a better version with the better version of the audio)
10. Take note of which playlists each file is in and manually add the new versions to the same playlists. I only have 2 static playlists, so this is easier than it sounds.
11. Select and delete the old files.
Hope this helps you develop a process that works for you.