Manage entity_id in data migration from M1 to M2

We are planning to migrate data from M1 to M2 and for that we are planning to write custom script because there are lot of customisation done on M1.

We have lot of stores available in M1, We are planning store wise migration, so for that we have a doubts.

• In sales orders table there is field available entity_id that is manage with other third party systems.

for this can anyone suggest us better solution that can be implemented?

Any help would be appreciated.