I'm having to make some assumptions because there is missing info in your post, but it sounds like the flex space doesn't have a separate door to the exterior.

Hi, at the stage of painting the exterior of the house.

Wind damage to the exterior of the property.2.

With its own exterior entrance, soundproofing, and hotel-like amenities, guests have a comfortable space without ever entering our living area.

However, you will likely have more maintenance without the HOA as now you have the exterior and grounds to worry about, as well 4 of everything on a 4-plex.

I can see doing the roof and starting on the exterior while they are still there but anything inside I’d probably wait on.

This can become a risk for both you and your ability to sell.As for things to talk to HOA about, beyond the permanent exterior colors/finishes, I would also ask about things like dumpsters and potentially port-o-let's that may be needed during rehab.  

Look at mechanicals, general condition, type of plumbing, exterior, roof, etc. - Repairs / updates are more expensive than you think.

The also have a product called Solo, that is a semi-gloss exterior/ interior paint.

Are they picking window style and placement, exterior cladding, color, etc?