Yes, if you intend to modify anything you should wipe the tracker, then deposit into HOME from the origin game. Just make sure you're not changing it to anything that breaks the Gen8/Gen9 correlations.
Do note that if someone decides to review the data with a fine tooth comb, they may notice oddities (like let's say they noticed PID EC is the same as something else in the logs, but oddly IVs are differently, or something), but realistically how likely would that be tho?