That article references California.2nd, I believe it's a misinterpretation of the new California security deposit law which limits security deposits to 1 months rent.

My question is, is there anything more I need to do to (i.e. issue a formal written notice of lease violation) in order to prepare for the possibility of keeping a portion of their security deposit to pay for eliminating the odor? 

Adding to the last point, ensure the new debt does not negatively impact your father's DSCR or other financial ratios in a way that might make it harder to secure the next loan.

Consider all the things that could go wrong and see if the lease addresses them: unauthorized pets or tenants, early termination, security deposit, lease violations, late rent, eviction, lawn maintenance, parking, etc.5.

Sometimes we do that to secure a deal if it's a deal breaker, but we don't typically visit the houses.

The rate might not be ideal, but securing the property now is crucial—you can always refinance later for better terms.

99.99999% of all lenders are going to come after the secured asset, not the entity's other assets. 

Also check your states Security deposit laws.

Efficient negotiations secured the property for $158,000 on favorable terms.

Furthermore, if I am understanding things correctly, RE investors use the equity in their properties to scale/secure more investments, right?