Even if they don't rear their ugly head for a while, they can and many times will come around and eat up a significant part of your cashflow with an immediate vengeance.I'd say your decision/s of what to do, depends on what your goals are.

Wouldn't that raise your monthly mortgage payment and in turn eat up what every gross rent you have.

Financing costs eat up a ton of a percentage

Like others have said; don't give them a dime, and take any advice with a grain of salt and do your due diligence to make sure they're not leading you on.When I am working or eating lunch or whatever situation and I have something that pops into my head (whether for my business or RE ideas) I always pop open google and type in "BiggerPockets [question]" and more times than not someone somewhere has asked the same question and has gotten a ton of great advice.

You might be surprised at how much they eat into your profit. 

It means I eat cleaning costs, but the headache of continuous late payments is not worth my time.A tenant that continuously pays in partial payments or the whole thing late means some month in the future it just won't come at all and you will be evicting them owing rent, possible damage, and cleaning anyways.

Flipping can up a lot of your time and like you said the short term capital gains can eat into those nice looking profits. 

My take away is that it is a real possibility our HAP payments may not be deposited, but we won't know until very end of month because they are not going to announce it until last moment.My question is if HAP payments not paid for Feb and let's say government reopens and payments resume in March, will we get missed Feb payments or just have to eat the loss?

you have to eat and pay staff.. 

It seems like you are doing work in several places simultaneously, which will eat up your capital quickly.