I used Scrivener for 7 years and used it to write/publish over 100 projects. However, I had a number of issues with corrupted project files, projects that took 1/2 hour or more to open or close, and projects that wouldn't convert from 2.0 to 3.0 format.

With any platform, the bigger the file, the higher your chances of corruption are. I did not store all of my notes and research materials in the Scrivener project file. If I did, they would have been even more bloated and I am sure I would have lost more work than I did.

I'm with Mackenzie Carpenter on using Obsidian and md files. Obsidian lets me store everything as individual files rather than trying to wrap them all up in one package, which reduces the chance of data loss. So does the fact that it is saving them in a very lean (txt) format. I write one chapter per file, then compile them to a docx document when I am ready to send off to my editor.

I store all of my notes and adjacent files in the same folder (Obsidian basically acts as an alternate file browser, viewer, and editor. These files are saved on your hard drive and can be viewed/edited by any appropriate app).

I have a wiki set up for each series.

My research gets moved to a central location once I am finished drafting each book, so that I can keep all related research topics together and don't have to remember if I found that article on DNA when I was doing research for book A or book J. Or was it M? Right now I have 118 topic folders in my research folder, plus a few one-off articles I wanted to keep handy. Saves a lot of time when I want to go back to fact-check something or to write about a topic I have already researched in another book or series.