Incident analysis - especially where explosives are concerned - is absolutely something the CIA does regularly. (As is causing such incidents.) If I asked the CIA to determine if something was enemy(ish, in this case) action, I'd expect to get a fairly detailed report explaining why or why not back.

I'm skeptical until they provide some details on the FOIL documents received.

The NTSB worked for four years and released a report, as expected.

Wouldn’t the CIA first ask if you needed it to be or not be enemy action?

Sure, if you come to the CIA with "we need you to fake a report", they'll likely fake a report. In that scenario, though, I strongly suspect the 95% reconstructed fuselage wouldn't have been permitted to be a NTSB training aid for two decades afterwards.

How many other air remains had such done to it? 25 years seems a long time.

MH17 was similarly reconstructed.

https://www.reuters.com/world/mh17-aircraft-wreckage-viewed-...

Modern laser scanning makes retaining the original long-term less important, apparently.