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EGR in a diesel VW Bug - Critical?

I took my 2001 VW diesel Beetle into a shop (new to the area, first time there) to have the brakes checked and an oil change. The check engine light has been on forever (at least 4 years) and it’s always a “bad glowplug” code. I had the glow plugs replaced, still on. So I ignore it. This shop runs a diagnostic and tells me that at some time in the past, the EGR system was “jerry-rigged” and there are some hoses missing, something about a butterfly valve, and one hose end is now plugged with a large screw (he showed me). He says I have to replace the whole EGR system, $1000. Oh, and I need new front pads and rotors ($450). I tell him the last time the car was worked on was 15 months ago (got the manifold cleaned out and some other 100K mile stuff), and the car is running fine, other than some friction in the brakes. He insists that the EGR system in a diesel vehicle is ESSENTIAL to normal function, including the brakes, unlike in a gas car. He then looked me straight in the eye and told me “We take honesty and intergrity very seriously here” which instantly made me feel like he was lying to my face. I told him I didn’t have $1000 and took my car to a different shop where they replaced the rotors but told me the pads were fine. I showed them the diagram of the EGR system and they didn’t seem excited about the missing hoses or screw plug. I need to know, is this something I should fix or no???