I just got a similar report from a collaborator inside Waters itself pointing to the error:
System.IO.IOException: ERROR: Method not found: 'Boolean CompoundDatabaseClassLibrary.CompoundDatabase.InsertNewIonDetails(Int32, Int32, TransMode, Int32, Int32, Int32, Int32, Int32, Int32)'.
This turned out to be a compatibility issue between a DLL in MassLynx and the method export DLL Waters gives us to write their methods, which they were able to fix for their case with an updated DLL in MassLynx.
I asked what I should tell you and my contact responded:
"We looked into this earlier today and it appears that it can be case specific. The customer should probably contact her/his local support team to get an updated software version or a copy of the required library but we should probably review this on a case by case basis. I have cc-ed one of our GSS colleagues so that they are aware this as well and can provide assistance."
So, contact your Waters rep and hopefully they can get you a new version of MassLynx or a new DLL quickly.
Thanks for reporting the issue rather than just continuing to work around it. Always helps to get things moving.