This topic might also help you understand the recent changes.
As you discovered, Manager no longer automatically applies exchange rates that were created after the transactions were created. If you go to Settings > Currencies > Exchange rates, you will see something like this:
If you drill down on the Transactions count for each rate, you will see a list of transactions that fit within the scope of that rate. This does NOT necessarily mean that they use that rate.
This screenshot shows transactions that use the correct rate for the day:
This screenshot shows transactions that use a rate from a different date:
In the second example, you have an option to individually or batch select any transactions that you want to update, and then use Batch update from the bottom of the screen to update those transactions to use the exchange rate from the date matching the transaction. As far as I know this has to be done for every exchange rate entered. This could be a lot of work for you if you have different exchange rates for every day, and transactions on every day for a year. To my knowledge there isn’t a way to do this for multiple dates or rates in one go. I’m hoping that it might be implemented at some stage.