I did not receive the Kalas Helmet from Shakatu in my inventory, even I was able to register it to the lexicon. My inventory had spaces left.

Probably had setting enabled for black spirit to consume the items as you open them in Shakatu.

I never used this option and it is disabled. Also I bought 3x10 items and just the purple one disappeared, same as other items which I bought from the accessories shop

Putting it in the collection takes the item away. It even warns you.