When working on ArcGIS Pro, is tracking different versions of a gdb that contains a network and a topology dataset, using git, safe ? I am worried about data integrity.
I would say no. The FGDB isn't designed for this sort of thing, and even minor changes to your database contents or settings are bound to alter multiple files. These files are in binary, so it's nigh-impossible to visualize or understand the diffs these changes create.
Also keep in mind that settings and even feature data may be cached in the program, so when you change branches, you can inadvertently bring edits from one branch to the other. I tested it just now, and almost immediately ran into problems where I could not discard or commit my edits in one of my branches.
Git would probably work with a shapefile or something simpler. What's your use case here?