Hi Lestt,
I also have this problem with my app. I’ve made a post about it: https://community.shopify.com/c/Shopify-APIs-SDKs/App-uninstalled-hook-cannot-use-access-token/m-p/1184664#M67358
This is very unfortunate that Shopify doesn’t seem to allow use of the access token the moment the app is uninstalled. In my case it’s quite an issue because I need to perform a breif cleanup of an edited theme file 
Let me know if you find any updates or solution to this. I hope Shopify can allow the access token to be used briefly after app uninstall.