Modified Simple Theme to Hide Out of Stock items, not pages on collections & product dipslay problem

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We modified the theme because it was showing OUT OF STOCK items, we added a line of code in the display (forgot where) but it hid the out of stock products we have. But now, we are showing empty pages (pages still listing 1,2,3,4,5,6 etc) and our customers have to scroll through them to find products on these pages. See pictures

So what is happening is we load a collection on the webstore, it it shows 15 pages, but only shows 1 product per page, sometimes 3-4 or none at all. We want to have it back to normal where it showed 4 pages and the pages were full of products....

Any help would be appreciated!