Their are existing posts that detail that you get ride of this line of code to remedy the situation:
<IsIndestructible>true</IsIndestructible>
I did this with every building in my ImprovementDefs.xml file, saved it to the mod folder, and it worked for alot of buildings. Not all of them though. Any one that I couldn't destory was defined as 'unique' so I accepted it for what they were, carefully plotted slots that are indestructible. However when it comes to cities and metropolises, a few of my planets got invaded and they spammed these all over the planet. Now it's rendered useless and it's sinking my overall moral to a critical point. Yea, to me this is a bit game-breaking moment. No mod out there exists as far as I can tell.
If your successful in doing this, could you please upload the file and tell me what you did? Or just give some instructions? I would be so grateful!!
Thanks in advance guys 