Issues after Shopify went down recently

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Since Shopify went down a week or two ago. We have had issues on 2 of our webshops. They use different themes but the issue is more or less the same. Elements are set to opacity:0 for example and this causes many things to remain invisible. I also noticed that one of the console errors is that "jquery is not defined". This is on both websites. It is very weird as we haven't touched anything and the majority of the webshop works. Features like ajax add to cart and similar which I imagine also depend on jquery work. I added jquery from an external cdn and that error from the console was removed but that didn't make any difference when it comes to the issue with "invisible" elements. We use PageFly here and there on both websites and maybe pagefly got messed up after the "crash". I'm not sure in which direction to look for a fix. 

Please let me know if you have any ideas on what I can do to try and fix this.