I did this with my panniers. I've been using a combination of Jandd Mini Mountain panniers and Jandd Economy panniers, and I liked them except for the mounting systems. I will say that the mounting system on the Mini Mountain panniers are fantastic for off-road use because they are rock-solid, but they are a pain to install/remove on a regular basis. Since my usage is much more on-road, and since I use them locally for commuting and such, I wanted a quick-release system to make my life easier. So I installed the Ortlieb mounting system on both sets.

I considered just getting Ortlieb panniers, but I live in CA where it doesn't rain anymore, so waterproof was not a huge concern for me, plus I think the waterproof material can be a bit of a negative in dry conditions. Also, I prefer the zippers on the Jandds over Ortlieb's roll-up closures. Again, it was a frequency/convenience factor for me. I also like the side pockets on the Jandds.

For the conversion, I removed the old mounting system and covered the old holes with iron-on patches (carefully keeping the iron on the patch only since it would melt the Cordura fabric if it came into direct contact), then I installed the Ortlieb mounts right over them. It took several hours to get all 4 panniers done, but it was worth it for me. I love my "custom" panniers.