I think the Anhalter Bahnhof is possibly the most famous example.

 

I am going to leave the historians here to answer that one in detail.

I am just back from Germany and have been to so many major stations.  Some are clearly modern, some clearly historic, and some are very much a mixture.  Just what proportion of the "historic" are in reality rebuilds in the old mould, and what proportion of "modern" are actually nothing to do with WWII damage, but rather otherwise rebuilds of time-expired or outdated facilities, I would not like to guess.

A hundred years ago, railways were run with steam engines - horrid, dirty, environment polluting and inefficient machined that needed a lot of staff, services, supplies and attention to work and which had really slow and run-around times after each and every run.   There days -take a look at everywhere from Felixstowe to Severn Beach - you can find the best ever / most frequent service ever yet at a tiny piece of infrastructure compared to what it was in the past.   There IS a difference in many parts of Europe - many of the older stations remain - especially those below the "major" level - but in a sad state of decay / repair with new platforms plonked on the old infrastructure.

 
Were many very large German railway stations damaged by the bombers from the allied forces during World war two.

Which lead to them being totally rebuilt or having to be demolished because the had suffered too much damage.