The same thing happened to me in regards to Primary callings dissappearing, but I also had a bunch of duplicates in many other places in CDOL, that were not duplicated in MLS. I decided to do a Unit Data Refresh in MLS based on information I found at https://tech.lds.org/wiki/Callings
about 3/4 of the way down the page. I did this mainly to fix the duplicates in CDOL. However, to my suprise, this fixed the problem with the Primary callings missing from the Callings by Oranization list as well. Here are the instructions from the tech.lds.org page.
[INDENT]Correcting duplicate or missing callings
Sometimes clerks may notice duplicate or missing callings in CDOL. Beginning with the release of MLS 3.3, clerks can now fix this themselves. The steps are:
- Don't do this with MLS 3.4.3. Please wait until you have upgraded to MLS 3.5 (which will do a refresh request for you)
- Start MLS
- Print a report of the current callings (Organizations > Members with Callings)
- From MLS request a Unit data refresh (File > Request Unit Refresh Data...); this will include a callings refresh request.
- Do a Send/Receive to submit the request for a refresh
- After waiting for CDOL to process the request (usually within 15 minutes), do another Send/Receive to get the refresh.
- This will remove all of your callings and replace them with the data from CDOL.
- Clean up any duplicates and incorrect callings.
- MLS will allow you to see duplicates even in the leadership section.
- Do a Send/Receive to submit the corrected information to CDOL.
[/INDENT]Hope this helps!