Absolutely, I once needed five nights in a hotel, which comprised of
- 2x"2-4-1" deals booked separately
- 1xSingle Night

There is no problem. Just tell the hotel on arrival to merge the bookings together so you don't need checkin/out or change rooms mid-stay.

The only issue is an IT issue where the system can't understand anything more than 2 night stay.

I'm not sure what "risk" KathyWdrf is talking about? There is nothing in the T&C's that say you can't book two of these back to back.