For normal IP I usually just pulled the .XCI. How do I generate a new .XCI that uses the couple of modified HDL files for pulling into other projects, or what files am I supposed to pull into other projects instead; I want to be able to run a scripted build with my modified IP? Follow up question, if I have to pull this modified IP into a future version of vivado which files I do I need to source into my project?
After modifying the ip sources, you need to generate output products for the ip. Once, o/p products are generated, you can use the xci file in any project, it should automatically reference to the generated o/p products.