You can't blame the program for your lack of back up policy. If it's worth keeping you should be storing it in source control - there is no excuse for not doing that.
You say you leave your machine on all the time - what would happen if the machine itself failed? (hard disk failures are common) Who would you blame in this scenario?
Lesson 101 at Comp-Sci - back it up - or face the consequences.
I sympathize with your situation, but if there is a real issue with Soapui not behaving as you expect, then you'll need to give the team a little more to go on other than what you wrote in your post.
Start by providing the Soapui build number, the methods you used to save the files (save or save as), the expected behaviour, the pattern of the missing content - was it random or was it sequential?