Okay I figured I can just not update if this bug gets fixed and I should report it properly. So if you have a ship with full D-Mods and then you take the perk to remove 1 d-mod per month, it will take away the d-mod but your bonus points from having a junker ship will not be removed but rather will remain while the next d-mod down the line towards perfection gets added, giving you even more bonus points and will continue to add them until it reaches perfection. I did strip ship option in the refit room/station and I removed them, so they can still be removed manually. Anyway I for get the values... my Junk ship had 4 d-mods and I had a bonus of -60 giving me 60 more OP. After a month and with the d-mod removal perk I got the next perk at 3 d-mods, giving me -50 (I think) and then the following month I got the next mod of -40 d-mod giving me a total of 150 bonus OP, the following month at 1 d-mod -30 and then I got to perfection having a bonus of 180 d-mod points. Totally awesome. Like I said, I stripped the ship at one point and removed all my bonus points, (it was a mistake I didn't notice until it was to late). Not a bad bug in my opinion.