when upgrading to nightly builds 01/02 02/02 03/02 I get the message 'safe mode is set', and something like 'some functionality will be lost'
and indeed, flv movie files are not working anymore...

untill version 31/1 this message was not announced and movie files worked fine.

These are two separate problems.

The safe mode report is new to the nightly build, that is why you did not see it before.

The Video problem is different and will be fixed in the nightly build tonight.

I have fixed the Video problem and it should be in tonight's nightly build.

Safe mode set should just be a warning, correct? It should not stop installation or upgrade?

Yes, safe mode is a warning.