Reporting a bug. I have found a (somewhat painful) workaround though.
After I was done with all my manual entries I noticed that I was missing many transactions on Binance. New Syncs did not fix the issue.
To check if the issue was on the API side, I decided to create a new API key and add Binance as a second exchange. All the transactions seemed to have been retrieved on the new Binance wallet.
I deleted that new wallet and reused the same API key for the old wallet. Since I had done many tweaks/manual updates, I did not want to lose the work so I really wanted to keep the original wallet.
No luck, even with the new API keys, the wallet was still missing transactions.
Workaround: I recreated a new wallet for Binance, and I am re-doing the manual tweaks one by one. Not sure what was blocking the original Binance wallet from picking up those transactions.