Excellent, fnagle! Taught me a couple of things!
Just had the same deal with MobileDB (silent upgrade to 4.1.4).
I wanted to reinstall the desktop, twhich loaded 4.1.4 in RAM. I had 4.1.3 in flash. My plan was just to delete it as I wanted the PC "Syncher;" then noticed there was a slight "change" in version #. Crap.
JF won't allow you to move the flash version to RAM if there's an instance already there.
Deleted handheld/RAM app just installed, then moved "older" flash version to RAM, deleted again including saved prefs entries (full uninstall -from launcher, restored databases later).
Reinstalled "new one" to RAM, and moved it to flash. Restored ALL from CardBackup (good choice!) . . . and all was good (MobileDB didn't "restore," of course because it was in flash when the backup was made . . . where it belongs. Only difference was I made a small "tweak" to MobileDB but that's irrelevant to your problem (boosted dynamic stack request in TealMover before moving to flash, which improves its performance. Doesn't apply to D2G stuff, I'm just being accurate!).
Docs to go is a BEHEMOTH with a lot of "SS10jklxxsh" (I'm making that up, sort of) type files lurking about - and depending on your vrsion of SPRAT it enables you to remove not only docs to go but "other D2G crap" as well. There is SO MUCH stuff that I've thought of going back to TinySheet and foregoing synching spreadhseets at all - but so far haven't done so. Apparently there's a lot of cool new stuff in 7.003 which you'll enjoy; I just question the huge PC/Palm real estate investment considering all these "little files" created. For example:
THERE WILL STILL be one or two small files left behind which will/may be duplicated and I'm too busy now to look for them - but don't worry about it, martinr -- they're small. YOu can't get rid of them or at least you can't if D2G came in ROM with your T3. This is the whole reason I decided to GET JS/JF - the Normal Scenario is when you upgrade you have 2 copies - P1's "built in" 6.002, and your new 7.003!
Fnagle's post will help you - looks like a nightmare, but will go quickly and you should be fine. Just bear in mind from now on that when you UPGRADE, you obviously have to move OUT of flash to RAM, upgrade, move back to flash. Over time this will cause JFlash to "compact" but that's normal and a good thing. It will load the requested app after compaction. That's why I load apps I won't be upgrading (oldies/goodies) first INTO FLASH, SO THAT WHEN THE COMPACTION HAPPENS they're not moved around much or at all. Only the "newer add-ons" are moved, and therefore easily re-installed if necessary due to a "glitch." The only one that ever glitched was Agendus.