Note that we don't recommend anymore using common channel files, as could probably saw in the interface and the documentation:
https://neuroimage.usc.edu/brainstorm/Tutorials/CreateProtocol#Create_your_first_protocol
From your message, it is difficult to understand what you did to get to the current database state or what you mean with "standardize the channels".
If what you did is 1) using a common channel file (subject-level or global level), then 2) import your various files in the same subject, I guess the problem is that you override the channel file at each new file.
Please delete your subject, create a new one using the option "Default channel file: No", import all your files again.
If you are still having issues, please document step-by-step what you did, and post screen captures showing the files in the database explorer.