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for 3.5 scenarios I had read somewhere (trying to remember where - I think one fo the Guides - though haven't checked the most recent version of the guide) that you can (and perhaps should) use the stats for monsters that are in Pathfinder in favor of the stat blocks from 3.5 (and you can and should always calculate CMB/CMD for the monsters in any case).
Where things get messy is in scenarios that don't have PFS equivalents - or where the PFS monsters are of a different CR than the ones in the 3.5 scenario. There isn't much you can do there other than run the monsters as written but do your best.
Personally I wish Paizo would republish all 3.5 scenarios with full Pathfinder stats (which would be harder for some scenarios than others) as they did for Mists of Mawagi.
Since PFS scenarios are digital products I actually wish they would correct mistakes in scenarios - it might result in some degree of table variation (for folks who played prior to errors being fixed or for DM's who don't check their downloads for updates) but it would also allow for the updates for changes to goals and prestige awards (and in more than a few scenarios correcting the mistakes would address many issues with some scenarios)