I’m having a bit of a tough time making out the bevel in your second picture - the angle looks steep but not unreasonably so. Are you flat filing the backs of the cutting faces to work the burr? Here is a guide to determine the angle you should be aiming for.
I love flat files for sharpening larger blades like my axes and hatchets (they’re still finished with a stone) but tend to reach for a sharpening stone for smaller blades like scissors and secateurs. The wider face of the stone makes it easier to keep a consistent angle even without the use of a jig.