It turns out making it open the app prior works, though it still says the error even though the refresh worked. It says "show" or "close" and show just shows me the name of the shortcut "refresh all apps" with a red banner reading "this file doesn't exist" but everything works fine until I enter shortcuts app again. It may also be because I didnt have enough App IDs to refresh sidestore but all the other refresh's work. However this doesn't give me the same error so, has anyone else tried doing refresh shortcuts and how did you do it? Did you get this error? Is it due to it being unable to normally refresh itself? (My other 2 apps refresh fine, and its not a VPN issue)
#Refresh shortcut says "The file doesn't exist" edit: sideserver doesnt refresh? website lied?
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Support Ticket
We want to help you to the best of our ability, but first we have to ask and make sure you have taken the proper steps to installing SideStore before we can help.
Ensure The WiFi AND VPN Are On
Without WiFi AND the WireGuard VPN, SideStore cannot function correctly. Try toggling the VPN a few times.
Ensure You Don't Have AltStore
If you have AltStore installed as well as SideStore, you will only be able to install 1 or NO apps in SideStore!
Ensure Your Anisette Server Works
If you are using the official SideStore server you can check https://ani.sidestore.io/ in Safari for a text output.If there is no output, ping a Project Developer immediately!
**Make Sure You Didn't Use SideServer!**
If you used SideServer on Windows, SideStore will not be able to refresh itself, but other apps will install fine.
Provide SideStore Log Files or Screenshots
Please provide as much information about the error you are experiencing. You can send the minimuxer.log file from inside Files > SideStore as well as in-app screenshots, and that would help us diagnose your issues much faster!
Finally, The Hardest Requirement...
Patience! Please have patience with our Helpers and Developer staff, we are all open source maintainers who do all of this for free on our own time. Thank you!
What does "ensure you didn't use sideserver" mean? I had to install SideStore using SideServer initially, on windows. I closed it after, but how was I meant to do it?
Ok I have now found out that I was never supposed to use SideServer to install it, but AltStore. So.. why did I even download SideServer? Why was that the instructions on the website? And is this my actual issue or the fact that I used all my App IDs? Lastly, will deleting all my Apps free up the app IDs or do I have to wait out the 7 days and nothing will install otherwise? had to find out the hard way 
It turns out the error when refreshing in app and only for SideStore says "delete sideloaded apps to free up App IDs" then when you tap "view app IDs" it says App IDs cant be deleted. So what's going on? I'm kinda confused now.
In the forum im seeing that you can't even use SideServer to install SideStore on windows... so the website lied. ok cool. someone should fix that
Refresh shortcut says "The file doesn't exist" edit: sideserver doesnt refresh? website lied?
App IDs take 7 days to disappear
alright. ill use altstore method to install it next week
but is refresh shortcut going to work after that? and why is the website incorrect
Why it suggests to delete apps to free up App IDs is because refreshing apps reregisters App IDs
Sidestore is still in beta, certain things take higher priority
The shortcut doesn’t work in its current state, I have no experience with it so I don’t know how to get it working
The one on the website is slightly unclear, so I’ll dm you the one I wrote
alright good to know not to bother. ill just manually refresh once a week or so.
it was perfectly clear, just wrong
oh. but why hasnt the sideserver one been fixed