Well if you have to do it, you have to do it.

The main thing is that all of your various totals should match when presented to an employer. Basic equations like SE + ME = TT should add up. So when filling out an application you may have to manually subtract out sim time from TT to get the number they want.

Then when you interview you do not want to hand the person inspecting your logbook a puzzle... hand them a piece of paper listing any known issues or discrepancies with detailed values included. If they get puzzled they may start asking questions with a negative tone and that's not a good way to start off.

Obviously they are interested in honesty, but they also want attention to detail... the logbook is great because it shows your habits over the long term, especially paper books.

This is worst case, not all companies will be as rigid but many are, and that may be your dream job, or the only major which calls you this decade.