Welcome to Blesta ?
It's configured per system. Settings > Company > Localization
You can do that but their old invoices will be in Yen and their new invoices will be in USD. There'll be two currencies on their client account.
We took the mick out of whmcs in our billing brawl where if you change the currency on WHMCS it changes the symbol not the new invoices / services.
Yes you can either modify the invoice if no payment has been made or un-apply it and edit the invoice. There are other ways but that's the way I do it.