I use that same silicone stuff all the time to make repairs and non-permanent attachments of things to other things. I'm guessing it will work OK for this, but over time it might peel apart as shoes flex and move a lot. The silicone is flexible, as you said, but the adhesion may weaken with constant movement.
They make some stuff for this exact purpose called Shoe Goo... that may or may not work better. I've used it for off-label purposes like reinforcing the thin plastic shells of RC cars. It dries much harder but is still semi-flexible. It adheres strongly and won't peel off without a lot of force and a scraper tool. (Silicone can peel off using just your fingers).
Good luck, it might work out.