I have done around 100 de-lids and I have learnt a lot along the way. Because I record all my de-lids I am able to look back on a delid that my cause the console some issues, here is what I have found so far.
(1) You can actually cause a BGA issue by the way you open the console. I noticed by analysing my recordings that evertime I found it difficult to separate the MB from the heatsink, the force required to separate them can actually pull at the CPU and GPU substrate and this can in turn case a multitude of errors. The solution I have found is to warm up the console before taking it apart, the best way to do this is to turn it on for about 20 minutes, when the CPU reaches 75 degrees turn it off and take the console apart. Also its best to pull at the fan/heatsink away from the MB, if you pull the MB away from the fan/heatsink its more likey to pull at the substrate.
(2) dont heat up the CPU before de-lid, i have recently found out that applying heat and the adding the required force needed to cut into the sealant can cause BGA issues. So even if the de-lid looks successful with no scratches, the heat combined with the force is enough to cause issues with the CPU substrate.
(3) Don't pull at the CPU when taking off the heat spreader, the sealant must be fully cut, any force pulling at the substance may be enough to cause BGA issues.
(4) And finally, and this maybe controversial, once the de-lid has been performed I would rest the MB on a hot plate and slowly heat the entire board to 160 degrees over a 15 minute period. Then let it cool down naturally untill the MB is cold. This helps to straighten the MB and can prevent BGA issues which may already may be on the horizon. In otherwords the console may already be on its way out and the substrate is hanging on by the skin of its teeth. This procedure can prevent the pending BGA issue, and as we all know, prevention is better than the cure.