have you been changing any water in the last 2 weeks? If not, and it was me, I'd do a 100% water change, and make a point of trying to syphon the gunk at the bottom (you could even remove rock for this, syphon the water you set it in from the top, syphon your container, then refill it, and move the rock back in). then I'd give it another day or two, then just transfer the rock to the display (no water).
No matter what you do, I would not move any of the old water with it myself.
Edit: And OMG at no flow... I'd take it out, clean it well with a toothbrush and rinse it well, then put it back in with new water and lots of FLOW for a few more days, then transfer. Again, would not let that cycle water touch my tank if I could help it