A template contains all the attributes (layers, linetypes, building materials, surfaces, etc) for the project, as well as general settings (grid display, units, reference levels, etc) and the project structure (viewpoints, views, layouts, publisher sets, etc.)
If you copy/paste, merge, or hotlink module any elements from another project with differing attributes, they will also be merged into the file. This is typically known as attribute pollution and is not a good thing. You end up with extra/multiple attributes making management very difficult. Take a merged layer for example, it will automatically be turned of in all the layer combinations that were present in the template. So you will need to manually go and turn it on in all of them.
Unfortunately there is no simple solution for this. My rule of thumb is to apply the template only to new projects or if absolutely necessary, rebuild the model in the new template using a dwg of the plan as a trace reference.
It's a big topic and have been discussed many times before. Trying doing a search for attribute management.
This may also be helpful, although it is quite advanced.
Cheers,
Link.
