Thanks to Parik, we now know what the difference between the new version saves and the old version saves are for GTA IV.
Download pages for GTA IV saves now display whether the save is 220.127.116.11 and older or 18.104.22.168 and newer.
There is also now a modification option to convert save files to the old version. This will be marked as experimental for a while. You will still need to disable Games for Windows Live, such as with XLiveLess, on the old version to load these saves.
The new version of the game can still load old saves, so there is currently no plan to add a "convert to new version" option.