There is a new setting for SKU Tracking in Channels -> eBay, which is enabled by defaults.
Setting this to "off" forces the eBay listings to be created with UUID that was previously only used with Auction type of listings and does not set InventoryTrackingMethod = SKU.
Users can now change the eBay SKU (ebaysku) of the items without having to end the existing listings and in order to do so, the new SKU Tracking toggle should be disabled and set to "off". The eBay SKU values can then be changed and forced in for items that were listed initially on eBay with this setting turned "off".