Deleting files from your computer and formatting an SD card on your computer does not, and can not, harm your SD cards. The standards are quite stable and if there was a problem it would be repeatable, consistent and extremely evident every time over many connected devices for every person using such devices!
Lets just say, if that was truly a problem, most of the civilized world would pretty much halt and burn to the ground.
BUT... the OS "format" tools take shortcuts and never really hits every bit on the device (In fact it is quite difficult to do so on an SD device with standard tools.
FYI, the camera's format does the same thing, so formatting in camera puts you in no better position. Neither method is a good method for ensuring the a SD device is in good shape.
The SD formatter above (or similar Linux tool F3Read/F3Write) can explicitly force every bit of an SD to be written (not an easy thing to do with SD cards, SD hard drives, etc...) and will better exercise the card and help it mark any few bad blocks or flush out if something is truly bad and the card should be thrown away.
- Switch cards between slots. Does the problem still occur only with Slot1?
- Be sure to wait until the red read/write light on the back of the camera is truly out after turning the camera off.
- What size SD card is this (i.e. 64GB or larger, perhaps??) and,
- What OS are you using?