Here I follow the Inkscape(IS) recommended format for questions!

1. TL;DR; Open app, test with mouse - OK. Pick up pen and test, - OK. Go back to mouse - clicks have no effect in the IS window.
2. Start the app using mouse, it works fine. As soon as I click my pen,  mouse clicks are ignored in the IS active area.
3. Mouse pointer moves, tooltips appear,  but no clicks or wheel actions work across the entire window including the title bar (minimize etc buttons do not react to mouse-over).
4. While it is ignoring mouseclicks, if I mouse-L-click on the Desktop, the blue window title bar is greyed out as normal. If I then mouse over the IS title bar, the windows buttons highlight and work normally to minimise the IS window.  
5. Then, if I L-click mouse on the greyed title bar, it turns blue and the Windows buttons work normally to minimise etc.  
6. Hovering over buttons , all tooltips in the IS window work, but only one or two times, and the mouse has to be move outside the IS window to get tooltips to work again. 
7. After Inkscape app close/restart, mouse works fine until pen is clicked within Inkscape.
8. I can't find anything directly related on forum, manuals or on google. Wacom have some history with Inkscape though... 
9. Mouse and pen work OK with other apps e.g. MSOffice, Blender.    
10. Restarting the app with the same or any SVG cleared the problem until the pen is used, whereupon the mouse clicks have no action inside the app, except on the minimise etc buttons on the top.
11. EDIT: also tried unplugging mouse and/or tablet before and during use in many combinations, none made any difference. 
12. I can't find anything directly related on forum, manuals or on google. Wacom drivers have some 'history' with Inkscape though...  
13. Re-install tablet driver, then inkscape, same problem, Tried other mice incl Microsoft Basic Optical Mouse.
14. Kit list: Win10 Home 2004 , AMD ryzen 2600, 64MB RAM,  RTX2060, Trust mouse on default Win driver, New tablet Intuos 2019 Paper.
15. Inkscape downloaded from Inkscape.org.

So it is usable but clunky because I have to restart the app between open-intensive and mouse-intensive operations.
IMHO: I expected some interaction problems when using mouse and tablet, but this feels like a straightforward failure to merge the pen and mouse input streams; use the pen once and the local mouse  stream gets permanently directed to null... ie not restored on mouseclick/wheel althuogh mouse-pointer movement events are fine. 

Any ideas?

Preferences?

Hello Tyler
Yes, I tried each combination of the 'Use tablet...' and 'Switch tool...' options. Is this problem a Win10 thing? Do many people use mouse and tablet with IS on Windows?

I rekon there are plenty of tablet/stylus users on Win. 

Reading through the bug reports, it seems previous versions worked better, and the devs are chasing after it. https://gitlab.com/inkscape/inkscape/-/issues/1293

There are tablet driver settings I'd explore, but I can't say if that would be fruitful.

As workarounds, I'd consider an earlier Inkscape version or running under Linux (portable/dual-boot/dedicated machine).

@TylerDurden Actually there seem to be few on the forums using it the way I do. I draw on paper, importing, processing, re-exporting, drawing on the printed image again, iterate until done.  

I also really would love to know how to convert a regular filled (two-path) stroke to a single path which runs down the middle - a bit like like shrinking the distance between the two paths to zero so there is only one line of nodes not two.  

Linux: I use Blender and it runs the RTX2060 card faster under Windows. Ubuntu drivers do exist, but weren't so nippy when I tested it. I also removed my dualboot recently in a HDD upgrade  - but I do have a raspberry Pi400 so still Linux aware!