This is totally my opinion, but I think you can split this up into two entries:
Let's say you worked for Company A from 01/01/2000 to the date that it merged with Company B and became Company B. Let's say that date was 06/01/2000. I would break up the employment history into:
a. Start Date 01/01/2000 End Date 05/31/2000 with Company A
b. Start Date 06/01/2000 End Date <whatever> with Company B
Hope this helps.
-chatrathi
Std. Disclaimer: This is based on common-sense and not a deep, superficial, passing or intimate knowledge of any immigration law. If you are going to make life-altering decisions based on my posts, you are on your own! You have been warned!