How to distinguish the ABAP Code in include program into different TRs

Hello Friends,
  In our current project, two teams are working on the developments.  One team is for LES related developements and another team is for billing related developments.  As part of developments, same programs are sharing by two teams, example -
Include - MV45AFZZ, the userexits in include are using by both the teams for their developments
Now the issue was, since the same program is using by both the teams, and during program activation , system automatically includes the code in both the team TRs.  This was causing issue while testing and transport to other testing systems, since billing project is going live in next year and LES in coming november
Hence, we need to understand how we can differentiate the code which should not impact with other TRs.
Many thanks for your inputs
Best Regards,
Goutham

Thanks all for the quick reply..
I would like to brief more clear...
In current project, Team 1 is working for Logistics developments, Team 2 is for Billing developments.  As part of project plan, Logistics is going live this november
When two teams are working on the same include, Team 1 is activated the changes then the task is updated in their TR, later when Team 2 has made changes in the same inlcude then the task was includeded in their TR.    Now the problem facing was, Team 2 has developed statements like COMMIT  WAIT WORK  and also BAPI call etc... and these statements are causing performance issues and some other problems......
Recently Logistics related TRs are moved to testing system for testing, in that all the development TRs are moved into testing system and also code related to Billing project (Team2)  as well.... when we cross check the reason then it was identified that the same include is using by both the teams for the development.    Now we need distinguish the code specific to team whcih should not impact other...
Hope my explanation clear the criticality of the problem
Thanks
Best Regards,
Goutham

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