Hi. I am having a conservatory built and like you I have a manhole cover smack in the middle of the proposed floor. The company I am using are retaining it by fitting a double seat cover!
Only at the foundations stage at the moment so can't comment personally on how it will look/function. The idea is that the double seal will prevent smell etc but retaining the cover will allow future inspection if necessary!!
That's the plan anyway, hope this helps