When 7.0.1 came out, the same thing happened, but this time I happened to notice the HTTP Result Code 502, timout… that was happenning in the frontend and not in the instance, for some reason I didn’t think of looking there first (maybe because I only did it very late both times).

So I increased Apache’s TimeOut directive to a safe 900 seconds and now everything went fine.

Meanwhile, Björn Schießle from Owncloud gave me a very nice tip, for those who control the server and can ssh into it, one can do the upgrade with:

./occ upgrade

So there you go, nice and useful tips, two in one post.