I endorse everything Lorna says especially about checking ALL the Merge dialogue tabs.
It is easier to specify what will be merged rather than what will not be carried over.
Only the records in the GEDCOM file and its linked Media files will carry over.
Everything else in the .fh_data folder and the Public folder will NOT carry over automatically.
That includes saved Books, Cached 'hints', saved Charts, local Project Fact Types, website Packages, Plugin settings, etc.
If you copy some of those to the master Project they will still not work due to the changed Record id problem.
Local Project Fact Types, website Packages, and Plugin settings can be copied over manually and might be OK.
Saved Books and Charts are unlikely to work if copied over.