Based on testing Lightspeed has fixed this issue as of September 13th, 2016.
When products are not being created/updated in Ecommerce as expected, this can caused by a bug that effects the Reset Items to Defaults button in Lightspeed Retail.
Accumula has identified that this button currently has a bug. Pressing the button updates the pricing and tags displayed in Lightspeed, but the changes are not sent via the Lightspeed API.
We have alerted Lightspeed to the issue. Until it is resolved, Lightspeed recommends saving each item in the Matrix after tags are updated to ensure that they are sent to the API.
In cases where a large number of items have been changed using the Reset Items to Defaults button, our support team can trigger a full resync of your item data to make sure all of the data is updated correctly. Please be aware this can take several hours. How long it takes is directly related to number of items in your Lightspeed database.