I definitely could fill the metadata with a known dummy value indicating it is an invalid value. Also, deleting the geo point and creating a new one is a solution but is more expensive in processing and time to process. I fully agree that a geo point without metadata is a rare case usage.
It may be used to archive geo points but the metadata is no longer valid or necessary.
Also, without creating a data object relationship, is there a method of knowing when the geo point was create / updated?
For archival purposes, you could update the category of the geo points, that way they will be nicely grouped together.
To know when a data point is updated or created, you could add a custom business logic event handler for the corresponding API calls. Backendless would invoke that code any time it receives an API request to create/update a geo point.