So before I report this as a bug, I need to know first how slice information is stored; is it stored in the .osp, or in the .sfs?
In either case making changes to slice positions does not properly update regardless of saving your project. The only way to 'finalize' the changes is to use 'Bundle Sampler Programs' under File->Project Settings.
Was driving me nuts - I kept correcting slice timing to avoid pops/clicks and every time I reopened the project (even after saving repeatedly and changing other parameters on other modules in the project), the pops would be back as though I hadn't tweaked anything.
I'd really rather not have to bundle the Sampler programs just to sidestep this. There are a couple of gigantic piano soundfonts that take some time to bundle (which sucks when you're 'in the zone', besides driving the filesize of the project and AutoSaves from 541kb to 168MB), and the fact that I can't save on the fly without stopping/restarting playback is also a pain.
EDIT: Here are side by side mp3s so you can hear what I mean. The only difference between the two project files used to generate them is that in case 2, the Sampler Programs are bundled.
Case 1 - Unbundled & clicky.
Case 2 - Bundled & perfect.