I already put into sucrose gradient and flash froze several rat knee joints for IHC. I realize it may be too difficult to cut these into sections, however. Is it too late to decalcify these?
I would suggest decalcification (short duration) of few samples, at first. After checking for completeness of decalcification, with ammonium hydroxide/oxalate, the samples could be paraffin embedded.
Yes, you may decalcify but use EDTA for it, not mineral acids decalcify solutions. One possible problem is some artificial changes in sections, but may be not if it is enough dehydrated. Agree with previous answer try at one joint
After processing and embedding, you could also face your blocks and surface decalcify by putting your faces blocks in a decal solution for 10 to 30 minutes. Rinse the blocks in warm water and place on ice before cutting. You should get at least a nice ribbon of sections. If you need more sections, you can repeat the decal / warm water / ice again.