Train cancelled

Do not get a new booking. That is not necessary.

Remember, tickets are for routes, not trains. You still have your ticket. Your ticket is still valid. And you can use it to travel to Frankfurt. The fact that a train you selected during booking is no longer running does not change that. The railways cannot at their own discretion step back from the obligation to transport you to your destination.
And again: You did not buy a ticket for "Train such and such". You bought a ticket "Prague to Frankfurt Airport".

So the alternative you found you can just take, without having to do anything than find your train in Prague and get on. I would not however be stuck on going via Regensburg. Just do a search for Prague - FRA on Bahn.de and take the route that is offered there.

You might also look at taking the Flixbus to Regensburg. There is a direct bus from the Prague main station at 7:30 am, or one from the Prague Central Bus Station Florenc at 9:30 am. Both take 3 1/2 hours to Regensburg train station, so should get you there in plenty of time. Showing 17 to 19 USD right now.

https://www.flixbus.com/
That is the US site, but just put in Prague to Regensburg on April 13.

The problem with taking the bus as that you will need a new ticket, whereas for the train you do not need a new ticket. Furthermore, if for some reason the Flixbus is delayed and you miss your connection you will need to get a new train ticket, as in that case you cannot just get on another train...

You should not treat this as a "how do I get to Regensburg" problem, but as a "How do I get to FRA" problem. So just look up Praha - FRA on www.bahn.de, and take what is being shown there.

Thanks both for your advice.

@WengenK I’m just a little worried about taking other trains with my existing ticket because it has all the train details and timing but I get your point that the ticket is not tied to the train in my case since the change was due to the train company. I will clarify with the train company on this.

In this case the train company is "Cesky Drahy", and you are in luck, as they have a ticket office at Prague Main station.

Basically you have a contract of carriage with the Czech and the German railways. Somewhere on your ticket should be listed the "Transporters" (or if it is in German "Befoerderer"). Irrespective of where you bought your ticket, these companies are responsible for getting you to Frankfurt. Starting of course with CD, because it is on their trains that your trip starts.

And railways are obliged by law to provide you with an alternative if a train is cancelled. So in your case, because EX358 has been cancelled CD (the operator of that train) must provide you with an alternative. But I am pretty sure that were you to go to the station and ask what alternative they will probably point you towards those trains you already found.

Trains operate very different from planes. Trains do not have passenger manifests. There are no check ins. Your entitlement to be on a train is solely based on you being able to prove you have paid. That is what your ticket is. Your ticket entitles you to be on trains on the route you bought the ticket for. And yes, it is now often the case that you get a reduction if you commit to use that ticket only on particular trains, but that limitation is dropped if those trains are cancelled. Your ticket now defaults back to how tickets are supposed to work: They allow you to travel on a route, on any train on that route...

Thanks WengerK again for your reply, appreciate you taking the time.

I have reached out to the customer service of Czech Railway and they confirmed that there will be track maintenance, and for my trip, instead of a direct train to Regensburg, I have to first take IC 564 to Plzen, then take a free bus to Domazlice, and finally EX 358 to Regensburg.

When I clarify if I can take other route to Regensburg since I will be carrying luggage and the free bus might be crowded and not have storage, they replied that I cannot do that since there is free bus service introduced.

I will likely take the Flixbus for the convenience.