Operating system: Windows-10-10.0.17134 64 Bits
Graphics card: GeForce GTX 1070/PCIe/SSE2 NVIDIA Corporation 4.5.0 NVIDIA 431.86
Broken: version: 2.81 (sub 16), branch: master, commit date: 2019-11-12 13:28, hash: rB125257758007
Short description of error
If I click to add a new view layer, all collections which were previously disabled with the exclude from view layer become visible again. If you have hundreds of collections this becomes really problematic. Additionally manually unticking the exclude from view layer checkbox and then re-enabling loses all the hide in viewport settings (the eyeball).
Exact steps for others to reproduce the error
make two collections and disable one of them by clicking on the chckbox on the left of it in the outliner, now add a new view layer, the checkbox becomes checked again on the collection that you unchecked.
put a couple of cubes in one of the collections and hide them in the viewport by clicking the eyeball. disable with the exclude from view checkbox on the left, then re-enable again, now both cubes are visible in the viewport again.