First time poster here, excited to learn and grow in the forum :-)   I recently inquired about purchasing an off-market property, to which the seller's son indicated that the owner (his mother) did not want to sell because she was afraid of getting "destroyed by all the taxes as a result of a such a big sale." 

It would indicate a real major partner and an exceptionally high amount of deductible early expenses on a property with very low income, as in low occupancy.

Walk the units, look for consistent problems it could be an indication of a larger problem.

The guidelines indicated that tenants need to communicate about a reduction in pay or termination at work in scenarios where a tenant is unable to pay the rent.

My realtor friend was told by a lender that a memo came out today from the federal government indicating that loans for a non-primary house would go up by 200 basis points effective immediately.

In 2041 a new 99 year term will commence unless the unregistered ground rent is redeemed through the SDAT process (which takes several months, as you indicated).The lender should have requested an attorney opinion letter from title and that opinion (if drafted correctly) would have indicated that the lease will extend more than 5 years past the maturity date of the mortgage, satisfying underwriting guidelines. 

May indicate a dishonest seller.

As Tony Indicated, how is the loss valued is important.  

Our accountant has indicated to us we will have to have a different set of books for each LLC's, is this the only answer? 

As I'm sure you've seen, and as literally indicated by the impressive appreciation of your homes, Leander and those surrounding suburbs are quite hot.