Its told to never use quick toggle as it can ruin safestrap possibly. About only time is when you have issues with toggling safestrap.
And the files you are deleting are not the system files of the ROM in that folder. The only files in that folder are backups.
If you want a blank safe side, then just wipe and format the safe side in safestrap recovery. And install your new ROM. Which if you install a new ROM on this side you should do these steps anyways.
NEVER wipe and format the unsafe side using safestrap recovery (not that it should let you. It should be disabled in unsafe mode) you will brick your phone. As wiping the unsafe side would also delete safestrap at the same time.
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