I fail to see where data was "deleted" here.

Nobody destroyed anything; if it would have beed destroyed, you wouldn't have found it.

How long do you think it would have taken to check about existing 7.200 relations/polygons against some 312.000 in the import data to determine which one needs to be kept ?

Besides, did you read the entire page describing the problem ?

The whole point was that, some day, someone would be able to modify and possibly correct the data.

Which you did. Well done. I don't see what's the issue here.

Also here : wetland=marsh
See the section about tagging mistakes

Well, if you look at this page osm.wiki/Tag%3Anatural%3Dwetland you will notice that somewhere in the "How to map" section there is an entry about "wetland=marsh" which replaces "natural=marsh".
So that's why it was renamed at that time.