A lot of people ask me about save game compatibility between patches. It's actually not a problem if you use "Wrye Mash". So what's Wrye Mash and why should you get it? Here's a short description from the uesp wiki "Wrye Mash is a general purpose utility for managing and repairing mods and savegames. Currently it is the only tool that systematically prevents NPC doubling. It combines multiple mod-management capabilities making it one of the most strongly recommended utilities for both modders and players".
Download the program here: Uesp.net, and be sure to check the readme too (which can be found at the same page).
How to update your save-game to a new version using Wrye Mash
Here are the recommended steps from the Wrye Mash readme:
• You only need to do this if the new version of the mod adds or removes references from the game!
• Put both new and old versions of the Mod in the Data Files directory.
• Go to Mods tab (in Wrye Mash), right click on the new mod and select "Updaters...".
• Click on the "Add" button, select the old mod and click Open.
• Close the Updaters dialog.
• Go to the Saves tab, and select the save game that you want to update.
• Right click on the top of the Masters List, and select "Update".
• Right click on the old mod and select "Change To...".
• Select the new mod in the file dialog and then click "Open".
• The renamed master should turn bright green (instead of the usual pale green).
• Click Save.