I think the most plausible scenario for something like this to happen would be Charles IV granting a son of his the title of (Arch?)Margrave of Silesia, with all the Silesian duchies made vassals of this figure.
From there, all you need is dynastic good luck for Silesia to centralise a little and remain under a Luxembourg cadet branch, which makes centralisation of the kingdom of Bohemia impossible, especially if a separate line of margraves of Moravia also survives. When it becomes time for imperial reform of the 15th/16th century, pressure from these great magnates could result in the distinction between the kingdoms of Bohemia and Germany to be erased, so that they have equal empire wide status to other immediate lords.
Alternatively, in order to better centralise the bohemian lands which they can reliably control, the king of Bohemia/emperor voluntarily transfers Silesia from the kingdom of Bohemia into the kingdom of Germany, potentially as part of the reformation.