It would sure be nice for some software company or tuner shop to step up and do a video showing the entire process from start to finish.
From what I have learned on other threads, the bottom cover is stuck to the components on the bottom of the PC board by some very sticky thermally conductive heat sink compound. If the cover is yanked off, that is what causes the PC board to flex, and that can damage the solder joints, which are already compromised by the EU's insistence on lead-free solder.
I'm wondering if it would help to remove the cover gradually, maybe by inserting tapered shims into the joint and pushing them in gradually and giving the thermal compound time to release at it's own rate. That would minimize the amount of flexing.
I'm told that the old sealing compound is very difficult and time consuming to remove, so shops are merely putting more sealant on top of the old cured sealant, and hoping that will do the job.
Ask any decent mechanic what they think about the idea of not bothering to scrape the remnants of an old gasket off of mating surfaces before reassembly.
While it might keep moisture out, the bottom cover may well be further from the PC board than the designers intended, so that makes the cover less effective as a heat sink, and that assumes that shops are replacing the original thermal compound at all.
The worst case would be to leave an air gap between the cover and the components. Without the heat sinking they will overheat in operation, and eventually fail.
So there are the solder joint failures, which show up immediately, or very soon after the tune.
Then there's the heat failure, which can take months to show up. This is the failure that is seen as burned areas on the PC board.
Since I've never seen one of these jobs done, I'm speculating, but based on the information that I have gathered, and my own experience in the engineering world, it seems logical that the probability of success could be increased significantly by:
1. Taking extreme care when removing the cover to minimize flexing of the PC board
2. Taking as much time as is necessary to remove the original sealant from the joint
3. Removing the remnants of the old thermal compound and applying new compound of the correct type
4. Then, and only then, should the ECU be resealed.
If the shop insists on charging more for the job, so be it. That would be money well spent.