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I've done some experimenting and I found that it might have something to do with the $selfillum and $selfillummask. About 70% of the materials loaded this time. The ones that didn't load either had a fucked up name or had an issue with the $selfillummask. Here's an example of the logs:

[2017.06.20-17.55.07:758][354]LogMaterial: Missing cached shader map for material HammUErBaseMaterial, compiling. 
[2017.06.20-17.55.07:758][354]LogMaterial:Warning: Failed to compile Material Instance /Game/SourceStuff/Materials/BUILDINGSET057A_mat.BUILDINGSET057A_mat with Base HammUErBaseMaterial for platform PCD3D_SM5, Default Material will be used in game.
[2017.06.20-17.55.07:758][354]LogMaterial:Warning: (Node TextureSampleParameter2D) $selfillummask> Requires Texture2D

(2 edits)

Second verse, same as the first.

The $selfillummask node isn't used for most materials, so most of them compiled fine, but the $selfillummask param2D node got emptied, so you just need to put a random texture in there (it won't be used for most of them, and if it get used, it'll be replaced by what needs to be there anyway)

(while you're at it, check all the other nodes in your material to see if any of them got reset to nothing as well)