It would require a little more dimensioning, but if that is the only arc that causes an issue, you could replace that arc with a spline. A spline will flip back and forth with no issue.
Edit: I replaced the standard arc with a conic arc (rho=.5) and dimensioned the length of the straight section. I was surprised the that conic arc will flip. The spline I mentioned above would work, but wasn't very easy to change. The conic arc works great and the rho=.5 keeps it very close to circular.
Edit X2: The other thing I had to do was to add 2 short construction lines off the straight lines and make them equal. This sketch will fail if the dimension value makes the 2 straight sections vertical.
Fillet Problem.SLDPRT.zip 72.9 KB
it is because the arc would have to flip the quadrant or lets mirror the arc to the other side.
SW keeps the arc in the same origination as drawn. make sence to me.
only way to solve this is copy the sketch without arcs were they could have this happen and the add a fillet arc after the paste.
or just add a fillet feature after the sweep.