When I right click on the Scapple icon in the taskbar (MacOS Ventura 13.0) it lists all the file names I can open, including ones I have already deleted. I tried rebooting the computer and emptying the trash folder, but not sure what else to do.
How to reset a Recent Files list on a Mac is more a general OS question than anything relating specifically to Scapple. If the list gets jammed for some reason, you can typically just go into the software’s File menu, where you should find some equivalent of a “Recent Documents” submenu, within which should be a setting to clear the list.
If that doesn’t clear whatever is going on in the Dock, then you might need to do a more thorough system-wide reset of these lists. I always used Maintenance when it came to cleaning up things like that.