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Please help with our "incredibly disappearing products" problem

Please help with our "incredibly disappearing products" problem

Greetings from Japan!


So we've moved from a hand-rolled card that served us well enough from 2004 through 2015, to Magento, and it's been a challenge for us. Currently we're plagued by a strange bug that makes 15-20% of our products go out of stock in the store, and we don't know what the problem could be. Basically, random products (about 300 per day maybe) decide they've got 0 units in stock (or less than 0) even though we've got stock sitting right here in our warehouse. We've had to make Filemaker scripts that go through each product and load the page URL, looking for text like "404" or "restocking" and flag them for re-upload, but it's killing our sales. 


We think the issue might be related to scripts importing the order history for our customers so their new site order history will reflect their past purchases, but we're not sure. Has anyone experienced anything like this, a bug or setup problem that causes inventory to be "eaten" from the inside by magical creatures that can't be seen? 


We're running Magento ver. 



Any advice you can offer would be super awesome.