flexpreis For train travel

Will I still have a reserved seat?

Yes, but that reserved seat is still on the train you missed. If you want a reserved seat on the train you will actually take, you need to buy a new reservation.

According to the Bahn website, reservations are not cancellable.

I’m flying in to Munich and then taking train, I’m concerned if my flight is delayed I will miss the earlier train. Is it better to reserve the later train then take the early train of the flight is on time?

The DB site should be useful -
https://int.bahn.de/en/offers/saver-fare-flexible-fare/flexible-fare?dbkanal_007=teaserBlock_1-5_link_flexpreisbullets

"I’m flying in to Munich and then taking train..."

To where? What day of the week and what time are you scheduled to arrive? How many persons traveling?

MUC airport is served by regional trains. If your train trip is feasible by regional train only, then you have no worries, basically. There's no need to pre-purchase such tickets, they are not tied to specific trains at specific times, and discounted day passes are available on the spot, as a rule. The details I've asked for would be needed to determine whether regional train tickets will work for you, and how.

Going to Zurich

I’m flying in to Munich and then taking train, I’m concerned if my flight is delayed I will miss the earlier train. Is it better to reserve the later train then take the early train of the flight is on time?

I have the same question (especially because the price of the initial ticket varies depending on the time).

Regarding seat reservations, will we have to pay to get seat reservations on the earlier (or later) train? Is that fee always the same, or does it vary depending on the time and day.

Why aren't you flying to Zürich if that is your destination? Flex Preis tickets are expensive, so you will probably end up neither saving time, nor money...

But other than that, yes, a flexpreis tickets is good for, if I recall right, two days. So miss a train, just hop on another. On the cross border trains to Zürich however this summer reservations are compulsory, so when you book you will get a reservation, and DB has mad a bit of dogs breakfast out of this. There is no simple way to change your reservation except by going to the ticket office...

Regional only won't work for Zurich.

With a lengthy time cushion in Munich that helps ensure making your pre-scheduled train in the event of flight delays, the saver fare will work for you for travel that same day.

If you were able/willing to spend a night in Germany, you could use regional trains (all are time-flexible) on arrival day to reach an overnight destination on the train route from MUC to Zurich (Munich Hbf for example) and proceed to Zurich the next morning by high-speed train. Saver fares for the entire MUC > Zurich journey can be found for this strategy by employing the stopover feature at the DB itinerary search page. Sample schedule using a departure time of 15:00 from MUC with a 15-hr layover in Munich proper...

Lv MUC 15:04 > Munich Hbf 15:43 (or any other regional train journey that same day.)

Lv Munich Hbf 6:54 - 10:16 Zurich (direct ECE train)