Basically, you shouldn't have different tables for different companies - you have have one table which contains a foreign key link to a separate table which just identifies the companies:
Companies
Id Description
1 Joes Wheels
2 Mikes Tyres
3 Simons Hubs
DataTable:
Id CompanyId EmpNo EmpName ...
1 1 101 abcd
2 3 101 abcd
3 1 102 qwer
...
That way, you can identify "genuine" duplicates, and extract only the info you need for each company using JOIN and WHERE instead of UNION
This also makes it a lot more flexible to add a fourth company next week if you need to.