Thanks for providing the detail of Geany and the system, but next time you can just copy from the top of "Help->Debug messages" to get it all in one go.
Certainly opening and closing projects with large numbers of files works for other people.
First thought from segfault is running out of memory, you don't say how big your files are, but in-memory files use about 2.5-3 times their size to accommodate highlighting and symbols and editing space. And at save it takes a copy from the buffer to make it contiguous, and if encoding to non-UTF-8 makes another copy which is then written. Whilst these copies are freed that doesn't mean the memory system will re-use them, that depends on their sizes. So memory use is likely to grow during saving many files.
Since it doesn't happen to anyone else, can you run Geany under gdb and when it fails get a backtrace `bt` and paste here, note you may need to press return several times to get all of it.
The apparent leaving files open (actually they are closed and opened again) happens when the user session file list matches the project session file list. See #267.