Maybe this link can help you.
Traktor Crashes – Native Instruments (native-instruments.com)
Let me know if it helped.
By the way, next time the files delete themselves inside Traktor, make sure you make another folder and make the duplicates, in case you lose them.
Impacted in which way...?
Check the "Audio Setup" settings. Maybe the sample rate, latency or if on windows the device have changed. On windows it sometimes switches from ASIO to windows WASPI or vice verca.
Do you think that for the built in sound card, I've to chose the sound card of my computer or of my Traktor?
Does not matter. It's just a fall back if your Traktor controller is not connected.
Also, for the multi core processing, is it okay if it's activated?
Yes, should be fine.
Settings also look fine. I always use ASIO on my s4 mk3, but in theory wasapi should be fine too.