Something doesn't seem correct. What Estimating software are you using?

To answer your original question, yes, the CID number can be scripted and that'll be able to be run on previous jobs.

That being said, there's very few reasons tyhe CID number should be changed to anything other than it's default wqhich is the pattern number. 

Changing the CID # can have very negative consequences to other aspects of your software functionality. If you have other scripts using them, reports, filters, etc, that all can stop functioning or function incorrectly.

If your estimating solution requires you to change all the CID's you should find a new estimating solution as it's not a sound approach.  Typically, an estimating software would be referecing some other unique ID or product code. Harrison Code, UPC, etc.