About your first issue, would you use two screens? If it's the case, doesn't the program behave better if you close the 3D view window after moving it on the same screen as Sweet Home 3D main window?
Otherwise, you could attach the 3D view to the main window by removing the line

I'm using a second (big) monitor on my Mac where I'm working with the main window and 3D windows side by side.
Trying to re-attached the 3D window to the main windows leads into the same described, unresponsive behaviour.
Now I found: if I close the main windows first, then the 3D view everything is fine and the program closes normally as expected.
--> I'll try to use that workaround from now on. Changing the property hinders my workflow a bite as I'm opening SH3d multiple times a day and like the side by side layout of main window and 3D view.

About the second issue, go the folder Library/Containers/com.eteks.sweethome3d.SweetHome3D/Data/Library/Application Support/eTeks/Sweet Home 3D/recovery of your user folder and remove the files you'll find there. An easy way to reach that folder is too choose the Go > Go To Folder menu item in the Finder and copy-paste ~/Library/Containers/com.eteks.sweethome3d.SweetHome3D/Data/Library/Application Support/eTeks/Sweet Home 3D/recovery (with the leading tilde) in the prompted dialog box.

Thanks a lot, that did the trick for me! Before I was having 5 instances with a total of 10 windows open and refused to close (force quit) SH3D as this added up more and more windows.

Thanks for the timely reply, I'm happy for now.
Let me know if I can get you any more infos so that you can probably find/fix this behaviour...