At present, there is an issue on Magento 2 with SKU's that contain special symbols, such as / and % in the SKU. The result is that they are not being passed back to Linnworks during the mapping synchronization process. If such SKU's are linked to inventory items manually, or via the Stock Item Linking import type, inventory updates will not be submitted to Magento 2, either, as Magento would still not be able to parse the special symbols within the SKU.
This has been reported to Magento developers already, however, there is presently no resolution to this. These cases have been discussed here:
One potential workaround that has been provided by an external source is the following:
It appears that this is an issue with Apache rather than Magento. You might have noticed that the 404 response codes are Apache generated instead of the usual Magento 404 pages. This is because, by default, forward slashes cannot be encoded in URLs without getting rejected. Add the option "AllowEncodedSlashes On" in either your global or virtual host config (or maybe in the Magento .htaccess, though this could be a security risk for users who would never make requests with encoded forward slashes).