In your case it’s a native LX flight that happens to be operated by WK, but it’s not a Lx codeshare that has a native WK flight. So, treat it as a usual LX flight. All LX flights that are operated by either Air Baltic or Helvetic are treated the same way.

Regarding LX flights that are operated by WK and which have prime WK number, here is the info from Miles and More webpage:

• On selected LX code-share flights ranging from LX8000 to LX8499 (operated by Edelweiss), you’ll get your miles, Points, Qualifying Points and HON Circle Points, providing the flights were booked directly with SWISS under the LX flight number. On LX code-share flights ranging from LX4600 to LX4619, you’ll get your miles as normal, but no Points, Qualifying Points or HON Circle Points. No miles or Points are awarded on code-share flight numbers MS9271, MS9270, AI7701, AI7702, AI7703 and AI7704 (operated by SWISS).