Alright, so inserted the exact number of messages i deleted on Aug. 2 in the same places/dates, that should bring message numbering and links back to the same state before i deleted that thread. As others have mentioned before there have been other inconsistencies in it before though, so you can most likely still find other issues but to the best of my knowledge they should be unrelated. Especially anything that is older than April 2012 should not have been affected by my recent change.