I had the same issue – all my variable products with over 20 variations showed up as “out of stock” on the detail page. The error is theme dependent and had my IT support change the following and all is in order….
https://www.8theme.com/topic/problem-with-variations-didnt-allow-to-have-over-20-variations/ – the second paragraph gives a sample of how it should be changed.
This explain the interface:
https://woocommerce.wordpress.com/2015/07/13/improving-the-variations-interface-in-2-4/
I see you have 5000 SKU’s with the same issue and wanted to help. Good Luck!!
