We are using Temporal Tables feature in Sql Server on multiple tables

https://docs.microsoft.com/en-us/sql/relational-databases/tables/temporal-tables?view=sql-server-2017

Is there any way to ignore the SysStartTime and SysEndTime columns permanently from both relational side and entity side of code gen?

Deleting the fields from the entity should work. But with the next sync they're likely re-added.

You might want to uncheck the 'Field property is public' setting, which can also be set in bulk using Bulk Setting