Hello philatelyny -
You can ensure that your store categories are available for you properly on the lister page by navigating to the 'eBay' page from the My Account menu and clicking on the Update eBay Preferences button, and your store categories will be available on the lister so you can post directly to them as well as your eBay category.
However, we are not aware of an issue with bulk relist causing the categories to be dropped when the items are relisted. I suggest that you file a support case from under the Help tab of the site letting us know a few example items of where this has occurred and the steps you take prior to posting so we can take a look into this.
While we do offer an inventory system within Auctiva accounts, it is not identical to the one that eBay offers.
- Craig