According to this HowToGeek article, as long as you don't put anything in the
Backups.backupdb, you will be fine.
The Time Machine only deletes files inside the
Archive folder and the files in it should be fine.
Relevant paragraphs from the HowToGeek article.
The easiest way to store files on your Time Machine drive is just placing the files on there directly. Plug in your Time Machine drive and open it in the Finder. You’ll see a folder named “Backups.backupdb”. Time Machine stores all its backup files under this folder. Just leave this folder alone and let Time Machine use it normally.
Place personal files and folders outside the Backups.backupdb folder. Don’t place anything inside the Backups.backupdb folder — Time Machine automatically deletes files and folders inside there to free up space, so you may find your personal files deleted if put them there.