BEFORE YOU TRY THIS PLEASE TEST IT ON A SMALL BATCH OF TEST FILES, IT'S BEEN AWHILE SINCE I DID THIS BUT PRETTY SURE ALL THE STEPS ARE IN THE CORRECT ORDER
I'm assuming that your are re-ripping you CD collection to flac. If so this is the way I did it in the past.
Rename all the mp3 using just the [track #] tag so your files will look like...
01.mp3
02.mp3
03.mp3
etc...
Before you start ripping, set your Options to send your rips to a temp folder and open that folder. Set your rips to be named using [track #] tag so your files will look like...
01.flac
02.flac
03.flac
etc...
In the [Notes] field type "DELETE", leave the other fields alone.
For the mp3 files that will be replaced today put "FLAC" in the [Notes] fields.
(If your using the [Notes] field use another field or create a new one)
Rip your 1st CD, Open the mp3 files that it will be replaced. Delete the mp3 files then move the flac files to the folder. Repeat this step until you are done with ripping for the day.
Go to your audio library and search [Notes]=DELETE. Delete the flac files it finds from your library.
Now search [Notes]=flac
Select all the files (Ctrl + A)
Right Click > Libray Tools > Find and Replace
Click Select None then check the Filename
In the Find What box enter .mp3
In the Replace box enter .flac
With all the files still selected
Open the tag editor and scroll down to File Type and change mp3 to flac
With all the files still selected
Right Click > Libray Tools > Remove tags
With all the files still selected
Right Click > Libray Tools > Update Tags (from Library)
With all the files still selected
Right Click > Libray Tools > Update Library (from Tags)
I would analyze these files again.
This will update your playlists and also you will not need to tags your files again.