Tax code when going from self employed to employed

A question about : Tax code when going from self employed to employed

I hope this is the right place to post this, I was hoping for some help regarding tax codes.
My partner has previously been self employed and paid tax via the construction industry scheme, but has now started working on the books for a company. His tax code is now 1000L but no tax at all has been deducted since he started working for them, presumably because he has no previous earnings on the books this tax year, as his tax return obviously hasn't been done yet. My question is, is this really how it's meant to work? Surely he should still have tax deducted from his earnings, even if he's previously been self employed?
He has queried it with his employer, but they're just saying everything is in order, but if it carries on like this, then he'll end up having not paid enough tax & having to pay much more next tax year..?
Would be great if someone who knows could explain! Thx a lot.

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