DB train schedule suddenly disappeared

It's hard to say without knowing more details. But in general, if DB cancels your train you don't need to rebook your trip. That means that your ticket (even if you bought the cheapest one) becomes fully flexible and you can take any train that day.

I initially booked the train EC378 09June 12:28 from Prague to Berlin. But it’s no longer showing on DB website anymore.

I booked the ticket through Czech Railway. And I’ve yet to receive any emails on cancellation etc.

Will I still be able to board the train?

It appears that there is engineering work on the line starting Friday June 7 until Monday morning June 10. There is a train replacement bus between Usti nad Labem and Dresden Neustadt. At Dresden Neustadt you take IC 2174 to Berlin Hbf. Adds about 50 minutes to the travel time.

So your ticket should still be good, just a PIA replacement bus along the way.

Would it be less hassle instead if I change my ticket to EC172 Hungaria 15:05 on the same day (09 June)? Is this train EC172 running as usual?

No. the rail line is completely closed for 3 days. Everything to Berlin uses a train replacement bus around the construction.

These things happen, especially over weekends.

Thank you so so much for the clarification. Guess I’ll have to take a couple of transfers to reach Berlin ;)

Taking a bus (S.E.V., in German) around a section of track that is closed due to maintenance is not really a rare occasion in Europe.

Since you can take any train you want on the route you can leave on an earlier train, if you do not want to arrive later than originally planned in Berlin.