The teeth are pulled after the spay/neuter if the stats are good. There is no reason to put a dog under twice for this unless there is a problem. The actual act of putting them under (when they first fall "asleep") isn't something I'd be doing more than once for no reason.
Intubation does cause irritation. Coughing is very normal and expected. I've read a few reports of tracheal damage that owners assume was from intubation. Haven't really seen confirmation of that. I mean, yes, damage can happen. It absolutely should not be collapsing the trachea. Not going to say it never happens. It isn't something I'd be too concerned about though. And I would hope all vets are intubating for these procedures!!!
A CBC and chemistry really should be done at a minimum. Anything else is pretty optional, but not a bad idea. I think a bile acids test would be good. there are different chemistries you can get (some include more than others). Depends on how cautious you want to be. Don't know what each one includes off the top of my head. Not a bad idea to look at clotting factors, but my guess is that would get into some $$$.
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