I have done the same, wash off as much dirt gently but I placed in net pots with hydrotan pellets. No problems for my ebb and flow and the water doesn't seem to have dirt in it. Hell, I have seen some vids where clones/seeds were started in jiffy pucks and then inserted into 3-4 inch rock wool blocks. They fit right in and the rock wool acts like a filter and wont let loose soil escape. I would not do that until you have roots coming out of the puck.
What ever soil you miss, I am sure will break loose and will get tossed out when you change your res.