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All of my mods so far are on the Steam Workshop, but there are a few on Nexus that look to be quite useful. My question before I dive in is are there any potential problems that I need to be aware of mixing and matching mods from different sources? And if I use Nexus Mod Manager to manage the mods from Nexus, will I have problems with my subscriptions from Steam Workshop?

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I had no problems mixing and matching, but I started on Nexus and moved to using Steam workshop. –  Lawton Jul 11 '12 at 19:58
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The problem you'll face are the same that what you'll have if you mix mods from the same source: some mods may be incompatible.

The only thing I can see that may be specific to the workshop is that workshop mods can take the priority, so if you have two mods that, for example, changes the same texture, the workshop mod may force its texture when updating itself.

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There are absolutely no potential problems as far as my imagination goes. In the end the mods are going to be managed by Skyrim's launcher (which ones are enabled and which aren't) with the potential help of Nexus manager (which ones are enabled + the order they are loaded in).

Of course, the number of potential compatibility issues increases exponentially the more mods you have enabled, but the same is true whether you get your mods from the Nexus, Steam workshop or both. Having the Nexus Mod Manager may help you resolve these conflicts by changing the load order (mods at the bottom take precedence over mods at the top).

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Steam workshop doesn't grab mod updates from Nexus and vice versa, so just be sure to use the application that applied the mod when you want to update that mod. Otherwise, they both do the same thing under the hood and their should be no issue from using both sources.

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If you can find on nexus, u should use the nexus mod as, like others said, the workshop may override nexus files, and with the lack on control over updates and mod order, it will be a pain to use. I just looked around and have barely touched workshop because of this. Though I would like to ask, why use something new, when the old one works just fine, in my mine's and many others' opinions, though I guess people can't initially understand how to operate nexus and give up quickly.

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