Here is the way I look at it. Warships are basically 3 parts, Interplanetary Drive, KF-Drive, and a Skyscraper.
When the Clans did their Refits, they just used the Interplanetary Drive and KF-Drive, everything else they just tossed, recycled, refurbished, then they rebuilt the Skyscraper around that foundation, reduces the amount of raw materials required. The Aegeii alone were pushing 500 years old, I imagine the Skyscraper portion of the ship was very tired, I am amazed any are flying at all after 700 years.
As to why, the previously mentioned Harjel, and expanded ASF Bays, Clan Armor, Elemental Sized passages, and in the case of the Liberator, York, Conqueror everything else.
The Clans were stingy they wouldn't have rebuilt/redesigned the weaponry, they would have fixed what they needed to, rebuilt the structure for Harjel, LFB, Armor, ASF Bays, and just put everything else back on. Also if you make it look different it maybe doesn't tie back to the SL in Exile, if someone runs across a patrol in the deep periphery and manages to escape back to the IS.
With there being so few Shipyards and many ships, I expect it would've taken the better part of the Golden Century to the Invasion to rebuild all the ships, and they didn't even get to them all, as witnessed by the naval caches plundered/destroyed during the WoR.
At this point, 20 years later it don't matter except for the sake of argument. :)