GI file opening failures with Unity 5.5.1f1

First, some background on our pipeline and how we use Unity...

Our application is for Windows (x64) and is essentially a game loader (we call it the shell) and a bunch of mini-games that run within that shell. The mini-games are not at all very similar by design so putting them all in a single Unity project would have made development quite cumbersome/inefficient with all the varied assets required for each game. So, we setup an automation pipeline that allows us to keep each mini-game in its own separate Unity project while still sharing code/assets back and forth between projects (without the use of .unitypackages since it would be cumbersome to have to build/import them as often as things change). The backbone of this sharing is done with SVN externals - each mini-game project "imports" the shared/core code and data/prefabs/etc. from the shell project in SVN so that we can have hooks into the main game framework, shared services, UI, etc. Then, at build time, we build each game to a set of streaming assets (generally just an asset bundle) and, via automation, copy that (plus any dependent scripts) back into the shell Unity project for the final build of the shell including all the mini-games. Obviously, this sharing back and forth relies heavily on meticulous handling of .meta files and their GUIDs to maintain each asset reference throughout all scenes/games. We have necessarily put things into place to push/pop render/lighting/quality/layer (and regrettably not tags since no API's exist to change them at runtime - hint hint!) settings when each mini-game gets loaded/unloaded in the shell. Also, the development environment allows us to create standalone .exe's of each of the mini-games if we want to for demos, initial prototyping, etc.

Now, the problem:

We were on Unity 5.3.4 and wanted to upgrade to the latest Unity. This had all been working in 5.3.4 and is largely still working in 5.5.1 except for one tiny (but VERY problematic) issue having to do with GI lighting. When we create the final build of the shell with all the game bundles imported into it, we get many sets of the following errors in the output log:

Failed opening GI file: '6c/6c443b8bce8cc503eca7e352de9c47ff.iws.sse'.
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Failed loading Enlighten system data for hash: 0x6c443b8bce8cc503eca7e352de9c47ff
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Error adding Enlighten system data: 6c443b8bce8cc503eca7e352de9c47ff. RadiosityData is missing.

The result is that our lighting looks very dark in many places. If we run this same configuration through the Unity editor (i.e. the shell + bundles imported) we do not get these errors and the lighting looks like we expect it to. It is just when we create the build of that same setup that the errors show up and the lighting is broken. The lighting also looks correct in the individual mini-game projects running through the Unity editor and if we create a standalone .exe in said projects.

I have scoured Google relating to the error messages we're seeing and have tried everything recommended including (but not limited to) running the final app as an administrator and purging my GI cache (before creating the game bundles as well as before creating the final build) to no avail. Also, I checked the location of the GI cache and those files are there (at least, after purging the cache and rebuilding, they were).

Can anyone think of anything new in Unity 5.5.1 that would cause this behavior to only start showing up now? I know this is an unorthodox usage pattern for Unity, but like I said, it had been working flawlessly until we tried to upgrade from 5.3.4 to 5.5.1.

Any help would be extremely appreciated as the next route for us is to step down version by version to find the newest Unity version that does not exhibit this behavior. We would like to avoid this (and the likely inability to be able to upgrade past whatever version that ends up being since we rely on this setup) if at all possible. Submitting a bug for this is not going to be terribly convenient since it really requires two full Unity projects to be able to test, but we will if there's a way to submit two projects to demonstrate one bug.

 

FWIW, I have started the step down version by version approach and the issue seems to go away at the most recent 5.4.x version (5.4.4). So it looks like something changed between the 5.4.x series and the 5.5.x series that is producing the errors listed above. It would be very disappointing to have to switch back to 5.4.4, but we have to have something that works asap - hoping someone at Unity has an idea!