Try using the Attribute Manager. This will allow you to add by appending the custom materials and other attributes from the other files.
If they have the same name as one already in the file archicad will add (1), (2) etc to them so they are all separate materials and you can rename them as you wish.
in the long term, when you want to customize a material for a project, copy one that is close to what you want rather than mess up the out of the box materials (and other attributes).
Have a template file that you then add to it all the customized materials and other attributes.
HTH
Erika
Architect, Consultant
MacBook Pro Retina, 15-inch Yosemite 2.8 GHz Intel Core i7 16 GB 1600 MHz DDR3
Mac OSX 10.11.1
AC5-18
Onuma System
"Implementing Successful Building Information Modeling"