I've had the same problem...in fact I still do with a few pedals. My mistake was to use too large pieces of velcro. The stuff I got seems to be industrial strength. The velcro sheets stick so well to each other that it pulls off the glue. I finally realised that I don't need to cover the whole pedal base with velcro, a small square on each corner is enough.
I've taken to unscrewing the bottom plate off my pedals, tucking the velcro in either side and screwing the plate back on. No glue, no mess, it doesn't come loose and I can restore the pedal to how I bought it whenever I want.
Yes that's damn clever, I never thought of that!