That's perfectly true. Creative mode can help.
Here is the final status of this. First I prepared my Unleashed world by moving liquids I wanted to keep out of tanks to capsules. I made a bit of clean up and partitioning of my AE system to make sure I would be preserve some stuff. If there had been a crash when opening the ME access terminal, I had the possibility to move storage cells full of misc items out of the ME drive and put the offending cells into a ME Condenser to get back the storage without the offending contents.
I then used a PatchMaker tool to generate an ID mapping based on mod configuration files. Using NEI dumps gave all sorts of funny mappings, like obsidian plates becoming slabs of marble, carpenter transformed into rain tank, barrels transformed into lasers from an assembly table (was crashing the game because of the barrel metadata incompatible with the laser), etc. The patch maker missed at least two mods, EnderStorage and ChickenChunks. I had to manually add mappings for the ids of these mods. I then removed the EnderStorage folder and ic2_cfg file from the world, after I read they can cause problems.
That done, I fed the patch to mIDas gold, the modified version proposed on this thread. The proper patch is salvaging all my barrels and most of my items. The patched mIDas or the removal of EnderStorage folder avoided the holes in my map.
Then I figured out I just need to preserve my main base. I didn't care about the rest, so I passed the converted map into MCEdit, selected the chunks containing the main base and pruned the rest. This will favor generation of new terrain and avoid any surprise, like getting veins of carpenters, finding an item that crashes the game inside a dungeon chest, etc.
After that, I was able to open all of my chests without crash, except one. I emptied it using an hopper+thrashcan. My AE network was sort of working, except of course I had to remove a bunch of patterns from the mocular assembler because of changed recipes.
The most badly affected portion of my system is the Thermal Expansion conduits and liquiducts. I had to redo pretty much everything, as liquiducts became floating pieces of hardened energy conduits while redstone conduits became floating leadstone conduits. Energy cells became Creative energy cells I had to destroy in creative mode (unbreakable otherwise).
As expected, my Thaumcraft wand was gone. My Thaumcraft room was all messed up: the crucible became an hanging middle block of an infernal furnace. I initially thought I had a block of lava right in my room. Destroyed in creative mode, this blocked became a blaze I had to kill/destroy as well. The infusion altar became warded jars and nodes in a jar that I destroyed. This is normal since Thaumcraft mechanic changed significantly in 4.1 version, and this new mechanic is one of the main reason while I switched modpack. I wanted to have fun with infusion crafting.
Railcraft Creosote oil bucket became cut firestones. I will destroy these since I should not have 15 of this rare item! However, I am a bit concerned by fire hazards if I get 15 cut firestones out of my AE network (from an access terminal). Will every surrounding blocks of wood and dirt set on fire in a few seconds if I hold such an amount of firestones in my inventory?
All Factorization barrels became Deprecated barrels that I will progressively replace with the new barrel style. However, hooking a ME storage bus to the top of a barrel is not enough anymore to let AE push and pull items in the barrel; it would require one bus at top for pushing and one at bottom for pulling, which starts to be a bit expensive and clunky. I will probably end up rearrange this as a system of logistics pipes.
So in conclusion, doable but not easy at all!
