It sounds (reads) like we're dealing with medical air from a Piped Medical Gas system ... and that the problem is in the plant room.
There we would normally expect a compressor charging a (large) pressure vessel. That large tank would have an automatic drain device.
In short, water should never make it into the pipeline (although I have seen this happen some years ago at a poorly maintained facility - until I intervened, I might add).
So, first things first:- the initial "problem" in the plant room needs to be addressed (and put right); then filters most likely shall need to be replaced. Depending upon details of the installation, the air drier (that is, if fitted) shall need to be checked out. Hopefully, the pipeline system can be drained and then clean dry air blown through it until the Engineer is satisfied that medical quality has been regained.
