> And flatMap isn't applicable here.

It's absolutely applicable, flatMap can trivially act as a filterMap by returning an empty array in the "remove this element" case:

     let p = (a,fn) => Object.fromEntries(Object.entries(a).flatMap(fn))
     p({a:1, b:2}, ([k,v])=> v === 2 ? [] : [[k,v]])

there you go.

You can even make the adaptation transparent by wrapping the fn:

     let p = (a,fn) => Object.fromEntries(Object.entries(a).flatMap((v) => {
         let r = fn(v);
         return r == null ? [] : [r]; 
     }));
     p({a:1, b:2}, ([k,v])=> v === 2 ? undefined : [k,v])

> My intent is to skip the entry with `b:2`. However, both map and flatMap error out.

Return an empty list from flatmap to remove the entry and a singleton list containing the new pair to alter it.

> Is this not the behavior you'd expect?

No. I would much rather have the existing function which has a very clear and straightforward behaviour and is not prone to silently misbehaving on buggy code.

> Note that without special treatment in fromEntries, there's no way for the mapping function to indicate "skip this entry".

I fail to see an issue with that. If you want to remove an entry, remove the entry.