It may be agreed that the fee for property 1 (in you example) could be 50K or really at an amount that the lender is comfortable with in keeping the remaining loan balance in place with property 2 as security.A lender will generally not increase their risk or exposure by releasing collateral, the idea is to reduce the initial risk level from that originally made.In your example, the loan of 100K is at 50% LTV using both properties.

Is the principal balance simply placed back into the IRA?

I firmly believe that the fundamental driver behind the "great recession" was over leveraged balance sheets in the household sector.

I do not know the attorneys you used but it appears certain things were missed.Glad you made a deal on it and bought low so you can hopefully absorb these unknown costs and legal expenses to balance it out into a win over the long run.No legal advice.

Take your remaining balance into something safe.  

I have done this several times before so know what to do and have the equipment to do it myself including tractor with hole auger to dig the six foot hole and front end loader to help set the 25 foot poles (not exactly fun or really safe to balance and tip up, but it works). 

Once I approve a tenant for my property, I require 1 month, non refundable deposit to hold the property until move in date, the balance needs to be paid prior to move in.

Equity and current balance along with interest will play into the bigger picture.  

The account balances and limits seem accurate within a month or so, but it doesn't seem to be updating my Transunion score.

I think you have to further specify whether you want to see appreciation or cash flow or a balance of both and dig into that particular city to understand the local market.Personally, I'm a fan of a blend.