I faced challenges with unexpected repairs during renovations, but having a contingency budget helped mitigate these issues.

You can strengthen your position by documenting the repair estimates and the potential loss of income due to the disruption in bookings.

Once you factor that in, your small loss is actually a bigger loss once you need to do any repairs or upkeep. 

Are these worth repairing?

They are pretty involved in making sure the property is updated and functional which ends up reducing the amount of $ offered, or if the property needs maintenance repairs Flock might not offer on it at all.

I make all necessary repairs as soon as possible, too.

Usually as long as their are no life threatening issues (no HVAC, windows won't open, no hot water), the housing authority will began to pay the rent and give you time to address the required repairs.

YOU decided that it was in YOUR best interest to do a remodeling at this time rather than just repair the access areas.

These are my options:a) Expensive contractor - wants $8,500 to demo and cap the two stacks plus some other brick repairs/repointing. 

MY LTR's are mid-tier for their market and have minimal cash flow at the moment so it all gets eaten up by  repairs and manager fee, my goal with these is mainly long-term appreciation and eventual cashflow as rents rise.