If you are on IMAP then they would still be present on both accounts, think is if you delete them all on one account, it will delete the ones you moved aswell. So you are going to have to de-link those accounts and make sure in the settings that the e-mails will be kept (or move them to local storage.

So once you know they are not linked anymore, you can delete all the mail from the account you don't want anymore. might be best to delete them directly from gmails web based server.

These accounts were never linked.

gmail do not delete as any reasonable person would expect. gmail store all emails in the 'All Mail' folder; it is the gmail archive. emails in any other folder are just labels, so they can appear in any folder including the Inbox. Removing/deleteing a label is not the same as deleting the actual email stored in the 'All Mail' folder.

If you delete an email via thunderbird, it gets marked as deleted but is not actually deleted from that folder until you compact the folder.

Unless you put the email in the imap gmail trash bin for gmail to empty periodically or upon exit if those settings are setup in Account Settings, then it will remain in the 'All Mail' folder even if it has gone from the eg: Inbox.

If you want to delete a load of gmail emails, put them in the gmail trash folder and then compact all folders. Emails should then be removed after the next synch with server.

Alternative, logon to gmail webmail to double check every once in a while and delete them from the 'All Mail' folder putting them in the gmail bin, so gmail can remove them.