Key Messages are lost in Call Key Messages after syncing to CRM Online when the number of Call Key Messages is greater than 25.
The user does not have Edit Field-Level Security (FLS) to the Entity_Reference_KM_Id_vod__c field of Call Key Message.
Currently, when the number of Call Key Messages is greater than 25, if the user has Edit FLS on the Entity_Reference_KM_Id_vod__c field, the app saves the Key Message ID into that field. Then when the record is synced up, a trigger on Call2_Key_Message_vod__c sets the Key_Message_vod__c field according to the value of the Entity_Reference_KM_Id_vod__c field.
Grant Edit FLS to Entity_Reference_KM_Id_vod__c of Call Key Message when the number of Call Key Messages is greater than 25.
Please refer to this guide if needed: Field-Level Security
CRM Help Documentation: Tracking CLM Key Messages