This shouldn't be a problem as long as it has completely dried out, especially the underlay. You could test this by buying a cheap 2 pin moisture meter from a diy store. If it is still damp it may be creating an odour. You don't want to be getting blamed for odour problems after the clean.
Before the clean take lots of photographs of all the shrunk areas, split seams etc.
Do this with someone who is either the foreman or manager in attendance.
That way there can be no issues regarding shrinkage after the clean. Preferably get them to sign a letter saying that they are aware that the carpet has shrunk due to the flood.
If you do this then a normal detergent clean using Clensan as a pre-spray should be adequate.
These carpets are usually around 5-6k. Do what I've told you or they could sting you and end up making you buy them a new one!