Hi,
It really depends on how you would want to configure the same or take it forward - but then please find my notes inline
1) If I could 'acknowledge' the interface as being down, maybe it would stop listing that it's a problem? If so, I don't know how to do this.
If you have set an alert on interface being down - you would receive an alert for just one time the same would be buffered in Solarwinds and hence it would not trigger a new alert unless and until the interface comes up and goes down again (but then reset condition on your alert has to be setup accordingly). The interface will be Down/Red - if you dont want the down status to be visible you will have to go with point 3 or 5
3) Is there some other way? If I remove the interface from monitoring, will it get discovered when they plug it in? If so, what's the proper process to remove the port from monitoring?
You can delete the interfaces but then Solarwinds will not automatically discovered the interface , you will have to add them once its plugged in. (Network Sonar Discovery is present to discover your network, but please go through NPM Admin guide - it might not be help much for your scenario)
5) I could set it to 'unmanaged', but I don't know the end date.
You can create a new custom property for interfaces called 'comments' and say suppose you dont know when the interface would be plugged in - unmanage the interface till a later date like 1 yr or 2 yrs ahead and mention the same on comments field 'Waiting for interface to come online', you can keep a check on such interfaces through orion reports and once they are back online you can re-manage them manually