Yes, this is a known issue when upgrading to newer versions of the Shopify Remix library. The problem is that your stored sessions in MongoDB are technically valid (not expired), but they contain data for an older API version or scope configuration. The new v4 library tries to use this stale session data, but the API rejects the request due to the version mismatch, leaving your app in a zombie state where it loads but cannot fetch data.
You are going to need to implement a self-healing check in your main loader. Wrap your initial API call in a try/catch block. If the request fails, catch the error and immediately throw a redirect to your auth login route. This forces the app to re-run the OAuth handshake, which will automatically overwrite the stale MongoDB record with a fresh, compatible session token.