Hi, this is what I would do.
First it is going to be easier to identify duplicates if duplicate files have the same name so I would modify the Rename Folder from Metadata masks and Rename File from Metadata masks in Preferences:File and Folder Correct so they match how the files are named in Collection A and then run Action:File and Folder Correct:Correct Filename from Metadata and Correct SubFolder from Metadata to remove any inconsistenties. Jaikoz does inform iTunes when files are moved/renamed as long as Preferences:Save:iTunes AutoUpdate is enabled, but there is not the same integration with other players.
However if these files are under the control of iTunes you may not want to do this is if you have iTunes configured to Organize your media automatically because iTunes renames files according to their metadata and its metadata to filename mapping.
Then fix Collection B and select Preferences:Save:General:Move Folder to root of Collection A (i.e C:\Music) so they are put into same location and run File:Save and Move. If filenames conflict the new file would be labelled file(2).mp3 ecetera.
Then repeat for Collection C
Now if you load all your songs into Jaikoz and run Delete Duplicates Jaikoz should mark duplicates for deletion. I think you want the default setting in Preferences;Local Correct:Delete Duplicates which will mark it as a duplicate if matches two songs to the same track on the same Musicbrainz Release. You cannot get it to prefer the file originally in Collection A to Collection B, but it will always save the highest quality file, i.e it knows that Flac is a higher quality format than mp3, and that a 192 kbps mp3 is higher quality than a 128 kbps mp3.
You can use the filters in Filters/Delete Duplicates Filter and manually choose which file to Delete. However now I look at this I realize there is no filter on Musicbrainz Id and MB Release Id which is probably what you want. If you only filter on MB Recording Id then it will mark a track as a duplicate if the same track appears on two different albums.
But you’ll have to do the above procedure in batches because Jaikoz is memory bound, with default memory settings you are limited to about 20,000 files loaded at a time.
Hope this helps