Usually that's fine. You'll count your cells and make the number equal between groups after they are suspended. But trypsin may cut some surface protein, resulting in the loss of epitope where the antibody recognizes. An example is MHC.
We've used CellstripperTM to remove adherent cells from wells for flow cytometry. It does not seem to affect surface proteins in the negative way that trypsin or EDTA do.
One potential way to maintain equal cell counts per condition is to set an event limit for each of your sample runs, e.g., use cytometer settings that stop analysis after x# of gated events for each sample.
I agree with Dominique. It is a good idea to keep your cell count per sample constant during your runs. This will ensure that you don't have a difference in the number of cells when you analyze your results. Good luck!