Migrating pst to google mailbox using google migration tool

Hello, I had a user that using outlook with a personal folder using Imap with Gsuite, I used the google migration tool to upload the pst file(mail that was in the personal folder so it would be in the cloud to be assessable online) and not all the mail moved to the google inbox, so I reach out to google and they told me to return the tool. I started to rerun the tool but notice in outlook that now it's not merging the folders it had created, now it created a new folder name outlook1.pst and all of the mail is moving into that folder. I am getting so frustrated with this due to the lady has many, many folders within folders. I really don't want to make a big mess but at this point not sure what is my best move. Any suggestions