Conversion to yahoo - emails now in both inbox and folders

I had 2 Comcast emails.  
Using an IMAP backup program, I did a test where I backed up one of the email accounts to my computer and then migrated it to the other account that I hadn’t used.

then I did the conversion to yahoo on the account I never used but now was identical to the account I did use.

I had organized my emails into folders so that I had maybe 10 emails in the inbox.

when the conversion was done, the inbox had a copy of the emails that were in all of the folders and the folders had the same emails.

It’s a nightmare trying to fix this.  If I deleted an email in the inbox it would delete it from the folder too.

I had to move emails from the inbox back to the folder and then of course there would be a duplicate in the folder which I could then delete.

has anyone run into this situation?

I am about ready to just delete everything on the yahoo account and seeing if restoring a folder at a time would make it easier to get things correct.

I am so glad that I invested a little bit of money to buy the IMAP backup software and did this testing before moving my main account to yahoo.