Just treat them the same, you don't need to rescale or anything. It's possible that some old scripts could error out (perhaps they have a hard-coded maximum value), but I've never run into such a case.

If you wanted to be extra safe, you could always use a simple script to replace any values of 41 to 40. It's extremely likely you won't have any issues, but if you have a pipeline using a whole bunch of various bioinformatics tools, it can pay to be paranoid.