Yeah this used to happen to me a lot actually
The first time I just emailed Scirra support with the new file and Tom had to manually update it for me if I remember correctly.
After that, it happened again, so I just uploaded the old version for the time being
What it ended up being for me was that, even though it didn't say it, the new file I was trying to upload was too large, so I cut back some of the audio and animations and it worked after that
It could be something different for you, though; I obviously don't know exactly how it works but yeah
Best bet is probably just to email them directly