I'd agree with most comments here, unfortunately I think this is a case of rushing. 3 weeks to fully cycle a tank does seem a little to quick, of course its possible depending on how it was done, also as already stated most freshwater bacteria won't live in saltwater, this together with the fact that you already have live stock would lead me to believe that the cycle isn't in fact complete.
As you've said rehoming the livestock which would be the best practice isn't possible unfortunately, which is a shame. I do feel that for the longevity and success of your reef this would be the ideal solution.
Now putting that all aside, it is normal for corals to behave oddly from time to time. Torch corals and hammer corals that have a number of heads will not always have all of them open simultaneously for a number of reasons, so I wouldn't worry (as there's nothing much you can do about it now) unless you see all heads closed up for a number of days. Although it would be advisable to test your parameters.
I have a torch that had 5 heads, it fell face down into the sand and was there however long before I came home from work. I repositioned it and one head died out.
That was about 2 months ago now and as already stated I'd suggest leaving the dead heads attached for a while as they can regrow, albeit at a very slow rate ime.
I've attached a photo of mine with the new growth circled. It's actually now got 6 heads ao seems to be doing weel and hopefully will continue to do so.
Good luck