ArcGIS Pro uses relative file paths, rather than allowing you to choose between relative and absolute file paths like ArcMap did. As an aside, there's an open idea to add that choice to ArcGIS Pro, if you finish your re-organization and feel that having absolute file paths would have made your life easier. That post may also have some idea/workarounds that could help you do this more efficiently.
If it helps, relative and absolute file paths are explained here.
Broadly, if you move a folder that contains an aprx and all the data referenced by that aprx as one unit, almost nothing should break. If you rename or move folders, geodatabases, shapefiles, rasters (etc), links will break.
A couple tips and tricks:
- Use the "find and replace" option to batch-fix broken file paths. Instructions here. For example, if your map has data in a "USGS" folder, and you rename that folder to "Elevation", links to your USGS folder are going to break. But you can find and replace "USGS" with "Elevation" in the file paths to repair all of those instances in the project at once.
- You can drag and drop folders from Windows Explorer under "Folders" in the catalog pane in Pro, and that will add a connection to that folder to the project. I think this is usually faster than browsing for it, especially if I've already got Explorer open.
- Broken layers can hide in layer groups if the group is collapsed. There are some good ideas in that post about how to make those more obvious without expanding/collapsing all your groups and subgroups (mostly by filtering for broken data or listing by data source).
Without seeing the state of the data, my guess is that this will be relatively painless at best (if you can move whole projects together) or irritating but worth it for having cleanly organized data in the end. You aren't going to irreparably break anything by moving it unless your cat stomps the delete button in the middle of the move, and so long as your files and folders are named somewhat intuitively, it's usually not that bad to track down what file the map was supposed to be referencing (although this gets worse with time: five years from now, future you will have no idea what you were thinking when you moved all this data, so don't let maps with broken data links fester.)
You can always pick a smaller project as a sacrificial lamb, move it, and see how it goes 🙂
