When using LightSpeed POS for a brick and mortar store and then Magento for the online store, you are bound to run into a couple of issues.
Until about a few weeks ago whenever product updates are pushed from LightSpeed, we had to re-enable stock configuration for all the products just so they can be added to the cart. Since we do not manage LightSpeed updates and we take care of the Magento store only we wanted an automatic way of re-enabling them. Working on a very tight schedule we threw in an updater that runs on regular intervals to update the stock configuration.