Switching backup devises then back. Does it duplicate?

My screen has been flickering with my iMac so I'm going to do a clean install and see if that solves the issue.
I wanted to back up my machine on two hard drives before I did this. So backed up on external drive 1 and then switched in time machine to external drive 2. There wasn't enough space on external drive 2, so I switched back to external drive 1.
Now it is indexing and saying there is no "older back-ups". Because I switched and then back, is it not recognising the recent back-up it did?
Am I better to just delete the folder from my external drive 1 and then start again. If time machine doesn't recognise the old back-up, then it will install a new back-up from scratch...problem with this is that there won't be enough space on the drive as there is already back-ups on there!

On your other drive you could use a clone application like SuperDuper! because cloning is so straight forward a process to accomplish a backup.

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