Does your lease state the tenant must comply with any HOA regulations?

Usually, this method gets tenant to comply.

I would have a gracious conversation with this person reminding them of the contractual arrangement for rent payments and hand them a Notice To Comply with your contract so it’s in writing - and in their file!   

Because of privacy laws the county would not even acknowledge that the office resided there, and the State Vital Statistics office would not give out a copy of the death certificate without a court order, also to comply with privacy laws. 

I'm still hoping they will just leave (I told them in the notice they can leave in 30 days if they don't want to comply and I won't file an eviction).

It's not your tax files where you might clean them out after 10 years, they cannot be cleared out.If the HOA is out of compliance I would not buy into the unit and if there and they don't comply with your legitimate requests you'll likely have to sue them.BTW, I used to own a lot of property in Houston TX which has no zoning so everything was in an HOA, I've served on HOA boards and been president of HOAs twice including my current residence in CO.

What makes you or your aunt think that a real estate agent is qualified to write up a legally binding contract that will properly protect her interests and comply with state laws?

You should also check with your Attorney on what might have to be done to comply with ADA (Americans with Disability Act) to determine if you have to upgrade any of the entrances, bathrooms, etc.On your question on the water use, if you get records going back to when there was a daycare operating they may show the difference in average water use before and then after the daycare closed.-

Don’t threaten eviction unless she doesn’t comply.

The validity of the lease may also be enhanced by evidence that both parties complied with the terms of the lease and that the rents were paid on time.You are not paying yourself a rent, but your Medical practice ( hopefully it is LLC elected as S-corp) is paying a market rent to your business entity, which is LLC.