Core Table alteration is prohibited

Hi

I have a use case where i need read orders from magento2 and process it. To make sure i am not process that orders twice and reading that order ones. I tried to alter sales order table by adding new field to it. This field I am marking when complete processing the data from order. I have this working solution. Now, Magento Team which says that adding new field is prohibited and I need to work on new approach.

So, Here are the questions I have and it would really helpful if some one can guide me. I am reading the orders from Magento2 using REST API. and I am new to Magento development with programming knowledge.

1. I didn't find any help on how joins can be used in API. If I need to make sure I don't re-process an order when i pick then REST order search API. I need create a separate table and store that order number in this table when order is placed using magento events. To read complete order information if i can make a join on this separate table It make my life easy and maintainable as well. Hence, is there any way to run Default Rest api using join of separate table?
if Yes, can you guide me with high level things to considered?
2. if no, any other alternative way you thing i can do here?

thanks,
Srinivasa