These documents are to be apply from local council.

If your property is rebuild accordingly to the new building plan which was approved by local town council, then it should not have been a problem to apply for CF.

Unless the rebuild was not according to approval or no approval was given for the rebuilt, then u might have problem with CF.

You can consult your Architect (if you have one, and with AR, usually they are hired to do submission for the rebuild building plans to local council for approval hence no issue on CF.), or ask for your contractor help (usually they wash hand on this issue).

Harder = not impossible.
Costly = better than no CF when finish building.

Dont be cent wise ringgit foolish.