Nenanah
Personally I would not, I'd be too paranoid.
I used to keep fish I had two fairly big custom tanks, when I would clean tanks I would never take the fish out because I would only syphon the gravel.
Cleaning the whole tank will get rid of the beneficial bacteria that your fish need in order to be healthy. Plus moving them to a jar then placing them back into new water could send them into shock due to temperature differences.
yeha...thats what i was leaning towards, i just wanted another few opinions to see if it was just me being paranoid or if i was right.