I migrated a website using the Cloudways Migration plugin, which has a number of important folders that had to be in the directory, although they were empty. When I completed the migration, the server immediately crashed due to the error log file being flooded with an error. It seems that those folders were deleted during the migration. I think that the Cloudways Migration plugin deleted them because they were empty folders. However, they were important, and a function that was looking for those directories could not find them, and triggered an error file that kept growing and growing.
Well, the Migration plugin shouldn’t be deleting directories, empty or not, but the script that needs those directories should be coded better. It should be checking for the existence of the directories and returning an error to the screen, killing the process and preventing the pile up you experienced. As far as errors go, this wound up being a useful one.
But - Cloudways really shouldn’t delete anything on migration, ever.