I didn't know HISE made any modifications to JUCE.
Mostly small getter / setter functions or other trivial things, but the most important change (which has no chance of getting pulled into the main JUCE codebase) is the addition of a custom Buffer for floating point values to be stored in the var class.
The process of updating JUCE is rather annoying (and each time it introduces some weird glitches), so I only do it when there's a real reason for it (also my cheap ass doesn't have a JUCE 7 license yet)...
Normally I'm doing these steps:
Fork the master branch of JUCE exactly from the commit that I forked it into HISE Copy over the JUCE directory from the HISE repo. This mark all my changes in the git. Review them again, do some cleanup and discard the changes that are useless (sometimes I just remove an assertion that annoys me too much) Create a patch from my changes Copy the current JUCE version into HISE Apply the previously generated patch file to reapply the custom HISE changes (sometimes I need to resolve merge conflicts).