"They are treated as separate businesses"

Treated as? Are factually two businesses? As separate entities, to segregate the ownership of the property? DBA?

"issued separate 1099-NEC forms for each property"

Properties don't issue paperwork. People, via their business entity, hire, incur costs, and issue paperwork. That's what happens when you are running businesses.

Have you searched the web:

property repair 1099

That will show you:

1. "over the $600 threshold:" The limit is when it reaches $600. Not when it goes over.

2. When the property owner is managing their own property, that typically is exempt for the informational filing, because that 1099-NEC provision was repealed in 2011, right when it was supposed to kick in (similar to the 1099-K issue right now).

https://www.buildium.com/blog/1099-for-property-management-2023-update/

If this is a Lacerte question, we need to know which form you are working on, the entity type, and are these a professional property management or property owner entities?