Windows 10 activation issues

Hi,

I have an XPS 13 laptop purchased around 2 1/2 years ago. While under warranty in the first year it developed a hardware fault and required a new motherboard. The dell engineer left an envelope with a windows 10 product key, though didn't really explain why. I had no further issues and Windows worked perfectly.

A few days ago I had a critical hard drive failure and couldn't get beyond the boot screen. I purchased a new hard drive and replaced. I then setup a USB drive using the dell recovery tool and reloaded windows onto the new hard drive.

Unfortunately, I am now unable to activate windows. The activation screen says I don't have a valid licence (though I was under the impression they are stored on the motherboard?). When I run the troubleshooter and say I recently changed hardware, it says it isn't able to activate windows on this device. When I try entering the product key I was given by the dell engineer it says it can't be used on this copy of windows (it is the correct version).

I phoned Microsoft - I read out the product key to them and they told me it is a pirated product key (?!). They told me to contact Dell. I phoned Dell and initially spoke to their out of warranty team, who tried to charge me a fee to give any help. I also tried speaking to the "in warranty" team but they would not help either. 

Can anyone please shed any light on this? I think this is Dell's fault - the motherboard was replaced under warranty and now seems to be the issue why I can't activate. 

Thanks in advance.