I set my incompletes to 9999 days.
No problem... skipping between versions; ie: going back & forward such as with the betas can have that effect. All you need to do is go to the Library window, select the incomplete folder, then select all the incomplete files & press the resume button. They will all show zero % downloaded until they actually start downloading again, upon which time their previous download % will show correctly.

Thanks for the help, I shall keep that method in mind, if it does it to me again.