They can go to any Credit Union with shared branching, deposit the cash or check, and their name is noted on the deposit. 

But I've also discovered that a couple of the local credit unions will refinance less than $50K with rates around 3%.And I've been working on the projected value angle with my dad, demonstrating how the values have been steadily increasing around here due to all the new development in the area, with an estimated increase of around 3 or 4% this year (though I'm not sure if that's considered good, mediocre, or what). 

The credit union doesn't offer fixed mortgages 

We hold it every first Thursday of the month at The Huddle up off of Fort Union Blvd.

Has anyone had any luck with smaller banks / credit unions to get a refinance in a similar situation ?

I have a HELOC thru my credit union and found a MTG lender to write the policy for my investment.

You might try a Credit Union or regional bank that holds mortgage loans in their portfolio (as opposed to selling them in the secondary market (eg, FNMA or FHLMC) as they might even look at an additional year to comprise a longer term history to average to get a better feel what you make with your flipping business.

Your best bets will be the local credit union or small bank in the area with your rental property.You'll probably need to use cash for the purchase/rehab, so make sure you understand their seasoning requirements to refi out once you have it rented.I know one lender in that area that will refi with only 6 months seasoning.

The unions have the hospitals by the short hairs out there.

I used a credit union if that's helpful at all.