> What actual risks are there and how can I avoid them (other than running
> 24/7 :)).
I think this warning means that reprepro knows about the volatiliy of the archives and can't continue a file that has changed due to version upgrade. Considering that it would be hard to copy a changing archive at once, and the more time goes by, the more probable the downloaded parts are deprecated and the progress is lost.
But I'm quite sure someone will (further) clarify that, maybe my guess already points you in the right direction.
Grüße aus Sachsen