If it says it wants to format both drives then you have either replaced the wrong drive or you have a hardware problem.
I have removed a drive and replaced it with a new one to test the NASs response and I just formatted the new drive and restored the array without problems.
I assume you marked the drives position before you removed them for testing and replaced the good drive back in the correct slot. If so what do you see on the web interface with just that drive in place?
Another thing, RAID 1 is NOT a backup so you should have a tested backup anyway.