Yes jiberjaber, your offsets should work just fine, or you can also use the "absolute" values you said as well. Since the focus offsets are relative to one another and focus changes are differences between the offsets, then it wouldn't matter to have all the offsets shifted by the same value.
As for which filter you use for focusing, that should not matter as long as the offsets are all entered correctly for each filter and as long as your focuser moves correctly based on the offset when switching filters. I say this because some focusers don't reliably have the same numbers for the same focus positions when focusing in or out and sometimes the focus drifts a little. So really the focus offsets can only be used as long as your focuser can reliably move by the same amount each time.