For my online PCT filing, I chose “automatic debit” as mode of payment. I have now received a search report informing me that the invention lacks unity. How do I make sure I pay the right number of search fees?

You should inform the EPO via the PCT-SFD (subsequently filed document) plug-in how many independent inventions you want it to search.

If you fail to reply, all the additional search fees due will be debited automatically from your deposit account.