In some cases, workflow update list / library wizard will update a column value even if it's not checked to update.
Column values are cleared when the workflow executes the update list / library events. This can also occur when using update methods on lists / Libraries from within SmartForms.
This is not a K2 issue, this is default behavior of SharePoint. If the column is configured to "Append changes to existing text"
To reproduce this issue with only Sharepoint:
Create a list in SharePoint with no K2, just add a 'Multiple line of text' column to the list and enable the "Append Changes to Existing Text" option. Add an item and provide a value, look at the version history that it is updated. Now edit it and only change the title. Looking at the Version history and see the other column is also updated.
To fix this you have to disable the 'Append Change to Existing text' option. If that is a requirement for your solution then the only other option is to populate the column in all the wizards with the previous value, otherwise Sharepoint will pass empty values as an update.