You broke something, all I can say with the info you provided tbh.

Valid gameplay reasons. (Exploits etc)

Edit:

May in fact be an issue of editing the wrong file. You should be grabing the xml's from ....DLC\EXP_2 Crusade if the xml you are looking for is not found here then revert to the base games folders.

The names should be placed in a file called ImprovementText.xml, which is located under the DLC\EXP2_Crusade\English\Text\ folder.  You can check the original file to find out how the names are linked to the improvements.

@Exploit as a design reason: this is clearly not the case for at least some buildings. I've checked the Improvement defs file for indestructibles, and most of them do not provide one time bonuses at all. And in the thread I've opened on this problem, no other valid reason was offered.

I agree that a mod that removes the indestructible flag for all improvements that don't offer one time bonuses would be... an improvement I would even go so far as to make Colony Capitals destructible, since they are often placed in suboptimal locations. But I suspect that might cause other issues.