It is a tough one and usually puts the ref in a no win situation when teams play funny buggers with their FR replacements.
I had a situation where a red team was being smashed in the scrum (lower grade) and appeared to feign a FR injury that mysteriously occurred at half time. Red asked for uncontested as they had no replacement FR. The opposition green capt complained to me they were faking it and they have another prop. All I could do was 'Capt, you'll have to appreciate my hands are tied as my concern is safety, so I have to allow their request for uncontested. I cannot assess their injury nor suitable other players. We can note it on the game sheet which I will sign but you'll have to take it up with the local union after the game". The capt was understanding of my position. Although I didn't think it was very sporting of the red team to call for uncontested, it was not my job to rule on that crap.
After this there was heightened friction between the teams for the 'games' being played so that added another dimension to managing the remainder of the game. Fortunately it died out as the green team went on to comfortably win the game. (Not sure if green lodged a complaint against red for their tactics, but the red team did drop out of the comp a few weeks later....due to lack of player numbers)