Something that is more annoying than anything is if I accidentally start soapUI a second time. When I then close off this second instance, the first one will start displaying an endless sequence of 'file <blah> has been modified externally' windows. With the size of my project, I end up killing the second instance, rather than clicking hundreds of times...
I can suggest a few things that would avoid this:
Allow only one soapUI instance at a time.
Allow a 'do this for all subsequent conflicts' option, like windows has when copying/pasting a bunch of files, some of which have identical names.