We have two payment files that appear to be stuck in the EFT queue , one with the status Processing Payments and with Queued. I believe the final status is Processed so would it safe to cancel this and do a retry?

You will need to Edit and cancel it. Then I suggest doing the next payment run in two halves, until you can see the obvious issue. Probably a vendor setup or missing data

the status with Processing Payments - would that indicate the file was never properly processed? If it wasn't then I can safely cancel and try the other one that is queued then retry this one.

You could check the Vendor Bills and satisfy yourself as to the status

Since this particular file that is stuck is AR - I can see an invoice and a related payment (status: deposited).. System note shows it was a Map/Reduce script that created the payment record. Does this indicate the PFA file was processed correctly?