Depends on how you root them, if you root them on a 12/12 cycle with out changing it, then they should continue flowering normally, albeit at a slower pace.
If you cut in flower, then root in non "12/12" then stick them back in 12/12 you are going to have a very confused plant with a much higher chance of hermie, in addition it will still have the funky growth because of the time it spent not on 12/12.
Duh - of course that makes sense! I've never tried that... Rooting must take some time at 12/12 too?