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Does there exist a script by that all what CK complains "xxx should be persistent but it is not" is to set persistent?


Dreifels

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In an ESP it doesn't matter as all references behave as persistent references, with Skyrim SE (1.5.x or 1.6.x).

In an ESM it depends how the temporary reference is used. If it's not used by anything else it's ok to be temporary. Determining whether a temporary reference is used requires cross-referencing it with other entities within the plugin, and possibly with Papyrus scripts outside the plugin. xEdit can show the cross-references within the plugin.

I don't know if CK is capable to building the same cross-reference as xEdit. I think it just uses dumb rules of thumb based on the reference base record type. For example, CK will advise any ACTI reference should be persistent, whether it needs to be persistent or not.

If a reference is temporary in an ESM and is used by something else, so it should really be persistent, something will not work correctly. A quest won't start or progress, an NPC won't move, a dialogue option won't be available, an NPC won't say their line, etc. and in many cases it will cause CTD at some point.

Unless you are debugging bugs with specific mods, there is no reason to worry about "xxx should be persistent but it is not persistent" - you're just wasting your time. 

Note that if mod A (or a vanilla master) defines a temporary reference which is not used by anything else in its ESM plugin, but mod B uses this temporary reference in its own plugin, it's mod B that is bugged, not mod A. Mod B must override the reference and make it persistent.

If you're trying to ESMify plugins and are worried about certain references needing to become persistent, you can try Persistentify Those Plugins which is an xEdit script that attempts to analyze cross-references. It's not perfect as it can still miss some references. There are other xEdit scripts such as ESMifyer and ESMifyer Addon which are limited to NPC references and use brute-force approaches, which can produces false positives or false negatives.

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