Thank you for your replies! Good to hear about other people having similar experiences, as this also made me quite uncomfortable.
I found out that in the original NDA I signed, there is a clause which says:
In the case this Agreement is terminated, the employee shall confirm the contents of the provisions in this Agreement which will continue to apply even after the employee resigns from the Company, and shall sign and seal, and submit to the Company, the written form prescribed by the Company under which the employee shall pledge that it does not hold any Confidential Information of the Company.
So this basically means that whenever I quit, I need to sign a document which says I have returned all confidential documents. I went to a lawyer specialised in IT who told me this is quite common, and that it doesn't hurt to sign as it simply confirms the NDA. So he read it through, suggested a few amendments and told me to then sign it which I did. In the end I feel much better after going through all of it with a professional.