Welcome to the forum!
With the phyical dimension, and the large number of objects showing, my best guess is that you're having a performance issue which is related to not having enough RAM to do what you've asked Inkscape to do.
The best first thing to try, is this. First, deselect everything. Next, File menu > Clean Up Document. If you look at the status bar immediately after you click, it will tell you how many defs were removed. (maybe hundreds or thousands) (If something is still selected when you click it, it won't show how much was removed, but it still removes it.)
That will help a lot, probably, but there may be more things you can do, so that you can keep on working on the doc. Because after a certain point, files can get too large for Inkscape to work on. First Inkscape will just be slow to react, or take longer and longer to finish something. But if you keep pushing it, Inkscape might even crash.
So for that reason, it's a good idea to set up Auto-Save. Inkscape Preferences > Input/Output > Autosave. You can try to remember to save -- maybe you want to save after every 5 steps, or every 2 or even every step. But it seems a lot of people just don't remember. So autosave is the best prevention.
And here's an article that covers all the other ways I mentioned, to allow you to keep working, even after you have clues that your file is reaching the limit.
https://forum.inkscapecommunity.com/index.php?action=articles;sa=view;article=35There's a chance you have a transparency issue. But by your description, I think it's more performance. However, if you can't get the contents back by Clean Up Document or any other measures, let us know, and we'll start looking for unwanted transparencies.
