Is there some reason why there are 43 less entries in the ships database? There are 436 ships in the databse in 4.86 and 393 ships in the database in 4.87.
I'm sure you didn't delete any ships, cause that would cause major problems, like character corruption if a player had a ship that was no longer in the database. The reason I ask this is that I develop tools for ADMINs and I usually include a ship.dat or universe.dat file with my tools to make it quicker to read the information.