Hello @ten12design
Schema Pro is not an upgraded version for All in one schema rich snippet plugin. Schema Pro does not store or handle the free plugin ‘s content/data. Both plugins are different, please refer to this article:- https://wpschema.com/docs/difference-free-plugin-and-schema-pro/
In schema Pro, you have to start it from scratch, it will not use free plugin schema markup. Plugins followed the different method to add schema on-site, free plugin follows MicroData format and Schema Pro follow JSON-LD format -https://www.envigo.co.in/blog/search-engine-optimisation/schema-markup-best-practices-json-ld-vs-microdata
So, It may affect if you removed the free plugin but you can use both plugins at the same time and once you get the result from schema pro, you can remove the free plugin.
Regards,
Uttam