multiple alias files

[devangee]

I have a question, and I can't seem to find the answer here.
I have one big project with several targets.
I use conditions and have multiple alias files.

My issue is this: in each of the alias files, I have a few of the same entries - almost the same.
The help ID strings are the same, but the help ID numbers are different. And these entries should call the same topic.
We have no control over the help ID strings and numbers they are automatically generated when we add content.

When I compile, I get warnings that the entries are in multiple alias files.
Is there a way to ensure I don't get the warnings and be able to test the context-sensitive mapping in Flare w/o issue?
I haven't checked the context-sensitive help within the program, but I'm not feeling 100% confident that there is no issue.