Sorry, I had somewhat misread your part on scopes. Don't all Hubspot accounts have access to Content Tools?
Free Accounts do not have access to any Content Tools, so if an Account was previously a paid one, installed your app, then downgraded, they'd see these 403 errors.
Going through your logs in your app, I haven't seen any 400 errors for that Account. The furthest record back was October 30th and that account was not included in those logs. That account does have access to Content Tools so it should be able to use your integration.
What you described in that the app predates scopes could very well be the issue. I was looking to see if there was any way for me to check historical data on a portal's installations, but couldn't find a way. Usually with a scopes issue, and if the account should have access to the tools your application is requesting, then uninstalling and reinstalling should work. Can you have them try that?