There are many EK flights that are scheduled and they hope will fly but end up being cancelled due to Covid, its not a EK thing, its world wide all airlines have the same issue.

So just that I have it right, your wife is departing from the EU to DXB then on to you in the Phillapines. A flight has cancelled and thus she now has a longer wait time due to the replacement flight.

Firstly she is covered under EU261 in that the original flight has been cancelled so can request a fee free refund. Also she probably has cover under the Covid cover for a fee free refund.

Secondly she is coming from Germany, which is Amber for DXB, so she can enter DXB if she wants, its just the connecting flight and ensuring her covid test does not expire if required. If she was coming from the Philapines then yes, she cannot enter DXB but thats not the case as far as I understand

P.s fair differance means little since, they change everday. You could see the cost of the same ticket now and if its less, rebook!