I’m aware of NOTAMS (notice to airmen) which are issued for launches of rockets, as for example mentioned in this answer. The same seems to be the case for deorbiting second stages (see here and here).
On September 8, a video taken by the pilots of flight LX178 from Zurich to Singapore was released by Swiss Radio and Television (twitter). It appears that the pilots were surprised (first thinking of a meteor) and thus were not aware of the re-entry of Soyuz MS-04 on September 3.
Are scheduled re-entries such as for Soyuz announced in advance and does it have consequences on commercial aviation?
-- external link to news article in German