Als er morgen nog bonen over zijn, nemen Anna en Sofie ze mee voor de lunch.

Because Als er morgen nog bonen over zijn is a subordinate clause introduced by als.

In Dutch, subordinate clauses usually send the finite verb to the end. So:

• main clause: Er zijn nog bonen over
• subordinate clause: Als er nog bonen over zijn

That is a very common Dutch word-order pattern.

Here er is an existential er, like English there in there are.

So:

• Er zijn nog bonen over = There are still beans left over

It does not mean there as a place in this sentence. It is just a grammatical word used when introducing the existence of something, especially an indefinite noun like bonen.

Here over means left over or remaining.

So bonen over zijn means beans to be left over / beans to remain.

This is not the preposition over meaning about or over/across. It is part of the idea over zijn, meaning to be left.

Nog here means still.

So nog bonen over zijn means still be beans left over.

In English, depending on context, this can sound like:

• if there are still beans left tomorrow
• if there are any beans left tomorrow

So nog gives the idea that some may remain from earlier.

Because the sentence begins with the subordinate clause Als er morgen nog bonen over zijn. That whole clause takes the first position in the sentence.

In Dutch main clauses, the finite verb usually comes in second position. So after that first element, the verb nemen must come next:

• Als er morgen nog bonen over zijn, nemen Anna en Sofie ze mee ...

If you started directly with the subject, you would say:

• Anna en Sofie nemen ze mee voor de lunch.

This is the normal Dutch inversion pattern.

Ze is the common unstressed object pronoun for them.

Here it refers back to bonen, which is a plural noun. So:

• bonen → ze

For things, ze is normal and natural. English learners sometimes think of hen or hun, but those are mainly used for people and in specific grammatical roles. For objects like bonen, ze is the usual choice.

Mee is part of the separable verb meenemen, which means to take along / to take with you.

In a main clause with a finite verb, separable verbs split:

• Ze nemen de bonen mee.

But in infinitives or subordinate-clause verb clusters, they often stay together:

• ... dat ze de bonen meenemen

So in your sentence, nemen ... mee is just the split form of meenemen.

Because they agree with plural subjects.

• bonen is plural, so you get zijn
• Anna en Sofie is also plural, so you get nemen

Compare:

• singular: Als er nog een boon over is, neemt Anna hem mee.
• plural: Als er nog bonen over zijn, nemen Anna en Sofie ze mee.

Yes, you often can.

For example:

• Als er morgen nog bonen overblijven, nemen Anna en Sofie ze mee voor de lunch.

That is very natural too. Both versions are possible.

A rough difference:

• over zijn focuses on the state: be left over
• overblijven focuses a bit more on what remains: remain / be left over

In everyday Dutch, both are common.

Because Dutch normally uses a comma between a fronted subordinate clause and the main clause.

So:

• Als er morgen nog bonen over zijn, nemen Anna en Sofie ze mee voor de lunch.

That comma helps show where the if-clause ends and the main clause begins.

Yes, Dutch adverb placement is somewhat flexible, but the original order is very natural.

Your sentence has:

• Als er morgen nog bonen over zijn ...

You could also hear things like:

• Als er nog bonen over zijn morgen ... — possible, but less natural in most contexts
• Morgen, als er nog bonen over zijn, nemen Anna en Sofie ze mee ... — this puts extra focus on morgen

So er morgen nog bonen over zijn is a good, normal order.