We had a similar issue, using a macro solved the problem for us as follows -
We are using the rules engine to assign postage services, however this means that orders that would otherwise have merged (satisfying current linn criteria) will no longer automatically merge. Is there a script available that will flag up orders that would merge on everything except postage service? I've seen requests for this in the forums but they appear not to have been actioned. If these could potentially mergable orders could be assigned to a folder we can then decide to merge manually despite different postage services.
linn "I think you can try to use the Macro in Linnworks Desktop - Settings - Macros - Add From Template - Order Management - Order Folder Assignment - OrdersToBeMerged. It will move orders with the same attributes to the folder"
You can then Set each criteria TRUE or FALSE depending on which conditions are important before multiple orders are assigned to the folder (to then be checked and merged manually)