Helpfully, there is a section titled 'Converting RCE [Red Clearance Edition] Content to PPE [Paranoia Perfect Edition]', starting on page 134. If you want to convert an ongoing campaign, start there. I will quote from that quite heavily. I've skipped stuff that seems really trivial, like 'illegal gear goes in a particular spot on your character sheet'.
Things that did not change
- Stats, Skills and their ratings
- Clone and Loyalty
- The core rules about NODEs (dice pools)
- Wounds and Health Boxes
- Treason Stars (except they're referred to as 'flags' a lot, e.g. 'Gain the Citizen-of-interest' flag)
- GMs still do not roll
- The missions are largely compatible - some mechanics have been removed (e.g. NPC stats) but they can be run as-is if you like (see the last section below)
- Character creation is mostly the same - it's still an exercise in screwing over the other players, and still has unresolved questions around edge cases
Things that did change
Troubleshooters
- All PCs now have a Service Group
- Personality adjectives are gone
- PCs now have Violence and Treason Buttons (i.e. less nuanced personalities, suitable for violent, drugged-up Reds)
- XP points can't be used to improve stats or skills; now we have Upgrade Points for that
- All PCs start with Guns +2 - nobody can choose a different Guns rating in character creation
- PCs start with 200 XP points, so the GM can take them away
NPCs
NPCs no longer have any stats. The GM is told to set difficulties as they see fit (remember, players do all the dice rolling).
The Cards
The new edition does not include the cards, but there are rules for using them.
Quote: "So here is our Official Famous Game Designer Wisdom for what to do with RCE’s cards: If you like the cards, use them." If you want to use the cards, there will be some information which is no longer relevant, but everything should be pretty much compatible (you'll need to recalculate initiatives, and gear descriptions have been tweaked - but does it matter if they're a touch off?).
Missions
Missions have a slightly different structure in PPE. It wouldn't break the game at all if you ran them as-written, though.
- They are all expected to have secret objectives (not all did in RCE; the name has also changed from 'secret society missions').
- PPE missions need a formal Mission Objective (one for each section of a published mission). This should generally be obvious, but you should define it for Upgrade Point purposes.
- Some secret societies have been changed or removed, but they are all detailed in The Accomplice Book, a supplement of optional rules and setting details.
- Achievements have been removed.
Setting
There are a ton of minor changes, and some fairly substantial ones. Canonically, any differences with RCE are due to Project Infinite Hole, and the Great Hotfix, which was planned well in advance and wasn't an emergency bodge job.
Changes not explained by the above events are few. Possible, "default" origin of Alpha Complex is now given. Knowledge of the Outdoors is not a treason. No "gotcha" from other players for knowing what a pig is. Exits from the Alpha Complex are not secret, just heavily guarded and won't open. The event that caused current situation is called Whoops and pre-Whoops technology now officially exists.
Misc.
- Initiative is calculated differently
- Hitting the difficulty exactly is a success (I thought it was in RCE too...)
- Armour works a bit differently
- When a PC Loses It their next clone has 4 Moxie (in RCE they didn't get their normal Moxie complement)
- All equipment has Success and Treason effects (in RCE only experimental devices did)
