ProTools is absolutely the most finnicky app I have ever seen. One of the few apps, and probably one of the even fewer high priced professional apps that can break when going up a minor OS version (like 10.4.8 to 10.4.9). I think they do it on purpose.
Anyhoo, the only way would be to back up/clone your drive, and do an erase and install the system you want. Then, I'm not sure how the Migration Assistant would work. I would presume that it would be fine for the most part as it doesn't transfer over base system apps that are installed, and that all of your applications and personal data would be fine; especially since it's from SL to L.
Then again, it is ProTools and I'm not sure how it would handle a migration.