I am anxious to hear the experts weigh in on this and as to what innovative solutions might resolve this issue, if possible!

If the contractor has money in their bank and bank decides to just take it and give to whoever disputes it or holds that amount until resolved, what then?

If you call with a problem, they'll say, "Oh you didn't purchase it from us, you purchased it from blah blah blah, so you'll have to get them to resolve your problem."

Use only professionals...document...document...resolve as quick as possible.

However, and while I want to believe that the Contractor will be able to resolve the $4,000 issue with the engineer, I am wondering if there is anything else I should be doing to protect against a potential lien.

@Derek DaunTwo pane gas-filled windows will resolve the issue.

I hope you can get this resolved.

While you could potentially sell with an existing problem, any buyer with a brain will discount the sales price to ensure they have funds available to resolve the issue.

I have disclosures the seller signs stating that the DUE on sale exists, we're not taking the loan out of their name and if a problem arises they agree to help resolve the problem. 

I went down the next day to get the SWO resolved.