I have managed to reproduce the core issue, which is actually in FStreamableManager (which asset manager calls to do the actual loading). The problem is that it’s not calling FixupCoreRedirects when failing to load a path. The loading calls on FSoftObjectPath itself already handle this properly, so I have filed UE-296063 to fix the issue properly. Nick and I will discuss the right way to resolve that.
In the meantime, you should be able to simplify your workaround by only calling FinalBundlePath.FixupCoreRedirects() instead of the slow FixupRedirectedAssetPath (which also looks things up in the asset registry). Or, if you resave the original asset that had the issue in the editor it should go away as that also calls FixupCoreRedirects. I think that might be why it was randomly happening, sometimes the cooker can save an asset multiple times and that probably fixed up the reference.