Well, the only further reference I found was from Medi-Cal, where they stated that the unlisted code 94799 should not be used for routine respiratory care...is the cleaning and suctioning being done by the therapists considered to be routine? That would be the question, so far as I can see. Not knowing anything about this type of coding, I can't say, but my gut instinct tells me that it is routine, and can't be billed.
Using the 31720 code won't work for endotrach's, based on the article you and I both found.
While I can understand the frustration of the RT's, if it can't be billed, it can't be billed. Have you contacted your major payers to find out what is covered under the 94799 code with them? That might be the next step here.