If you think about it in any industry less transparency and more friction in the transaction will increase fees/commission vs reducing them.I like the idea as an investor of having different agents, a team of agents maybe 3-4 bringing me deals, but I think less of that will happen now as all will have to have you sign some kind of agreement up front. 

But I know that the leaders are working on plans to fix it and they are very skilled and effective.

Contact the Title Company; it is their responsibility to 'settle' the transaction at closing.

I do not recommend paying any upfront fees, unless it's with a large bank that typically requires a good faith deposit on larger transactions.

The free marketing is not effective in a competitive market neither is the marketing strategy.

@Ankit Lodha, as others have pointed out, this sounds like a transaction you should be able to get done.

But, for instance, I sent them a notice of rent increase effective February 1 and needed them to confirm that they have accepted the new payment terms through our electronic payment system, and even after repeated notices, they are not responding.

2.What are the best and most cost-effective solutions for managing this potential long-term issue?

Some gurus tell practicioners of sub-to to hide transaction from the lender by saying the lender doesn't care as long as the payments are being made.

If you have the time to devote to it, direct to seller methods can be very effective, but will take ultra-patience and intensive work.