Plywood can be some funny stuff sometimes.
If it gets wet it can be just fine or delaminating all over the place, on the same roof with the same lot of plywood.
Whether or not plywood that has been wet needs to be replaced is determined on a case by case basis.
To remove and replace perfectly good plywood simply because it got wet is a colossal waste of resources and is not in the best interest of your customer.
It is in the best interest of the roofing contractor that likes to needlessly run up costs.
One of the purposes of roofing underlayment is to protect the structure from the weather during the reroofing/construction process.
It is not necessary to remove & replace felt because it got wet, in fact to do so would be another waste of resources for absolutely no gain whatsoever.
If a roofer wants to replace plywood simply because it got wet it's fine so long as the roofer pays for it.
If a roofer wants to replace felt because it got wet it's fine also, so long as the roofer is paying for it.
If said roofer attempts to charge the customer for unnecessary material removal & replacement this is very close to unethical behavior.
I trust a properly dried in roof over a tarp any day of the week, roof penetrations always get in the way of an effective tarp job.
The only time I tarp a dried in roof is in the winter to keep the snow off.
If tarps are working for you guys more power to you, there is absolutely nothing wrong with that approach.