Everything depends on the quality of the XDF file you are using to interpret the BIN in question. If the XDF is barebones (or worse, wrong) then you are pretty much on your own as far as knowing what does what and which setting goes where. In these cases I usually just compare two BINs from the same ECM with known features to confirm that a flag does what I think it does (for example, comparing an automatic and manual transmission to see which flags get set, or comparing a vehicle with a CCM to one without to see if there's a flag there). Sometimes "unset" is actually "on" with these, unfortunately.

As for why values change, that's usually either because you entered a value that goes beyond the limit of the cell (for example if the limit is 127 and you typed 255), or because you have TunerPro set to Hex display mode instead of Decimal and thus are entering values way higher than intended.

My concern is with that ARAR edit not working. A pre-90 Corvette won't have a CCM to get fussy over, so it should be relatively safe to edit. Which flags specifically did you alter? Also, were you using an XDF meant for $6E to make those changes?