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As far as deactivating plugins.. I didn't realize merged bashed patches did that so someone who knows more about that process will have to help you out there.
Also after going back onto wrye bash, the mods that are merged into the bashed patch have a + in their check box and it says when hovering over them "Merged into Bashed Patch"
Merging mods is a manual process of merging their file structures as you would expect, to lower your plugin count.
A merged patch is a bit different, its a patch that automatically merges mod data when you launch the game.
Im pretty sure that an SSEMerged patch requires the associated plugins to still be active.
Gopher has an excellent video on merged and bashed patches that explains it and shows the proper procedure far better than I can explain. :)
Pretty sure by doing that you have removed the Merged functions that you created in the bashed patch. Which is fine as i understand it you want to use SSEMerged for your merged patch anyway.
One of the popups windows after you hit rebuild patch has some checked option in the left pane, which include merge mods, and level lists and .. tweaks if i recall.
If you are using SSEMerged for merging then I think** you should uncheck all the options except leveled lists from this popup when rebuilding your bashed patch. Will save you the step of opening your bashed patch in SSEedit afterward.
You sound like you've got most of this working ok but just in case you don't know.. Gopher also says you want to deactivate any patch plugins you have active prior to making your merged and bashed patches and then enable them again afterwards.
An example would be something like
Bathing in Skyrim - Realistic waters two patch
As well as patcher mods as well, can't think of thier names at the moment.
What I do to be sure i've got them off is i start wyre bash and hit rebuild patch it immediately warns me about some mods that should be deactivated prior to making. I use that list to go threw my plugins and deactivate them all, then close wyre open sseedit and proceed from there to make my SSEMerged, remove its level list and enemies.
Then i (MO2) create the SSEMerged mod out of overwrite, then run Wyre selecting only leveled lists, activate it, return to mo2 and reactivate my patch mods.
1. All mods active in Wrye Bash.
2. Load order sorted with LOOT and applied.
3. SSEedit, create merged patch, delete ONLY the leveled lists from the merged patch, clean masters.
4. With SSEMerged active, create bashed patch, including any tweaks I've made. Allow Wrye Bash to merge applicable mods (in my case, usually only one...Rich Merchants) into the bashed patch. It will correctly deactivate Rich Merchants once it does that, though you should see a little plus icon, to let you know it's merged, not just inactive.
With both SSEMerged and the bashed patch active, back to SSEedit for "VeryQuickShowConflicts," where I click on each mod and see what has overwritten what, create overrides for anything that hasn't fully integrated, and then off to play.
My Xedit and wyre bash knowledge is still pretty limited, when i respond to threads of this topic Im always hoping that SMR or somebody will show up and fill in some of the no doubt many gaps in my advice :)
However youve been rather helpful so thanks I appreciaate it.
And yeah if SMR or someone got on here that would be great.
Thanks again
https://www.nexusmods.com/skyrimspecialedition/mods/164/?tab=videos#lg=2&slide=4