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Delete files, keep folder structure

We are an accounting office. To do our clients 'accounting, we use a service that collects all our clients' bank statements and puts them in an FTP folder.
They offer an FTP tool, but we must synchronize this manually. We would like to automate this.

The local AND remote folders are:
Client X / Bank account X / Statement01.cod

Client X / Bank account X / Statement02.cod
Client X / Bank account Y / Statement01.cod
Client Y / Bank account X / Statement01.cod

In every bank account folder there is also a pdf folder with a pdf of the bank statement

We just want the .cod and .pdf files to be moved (not copied) to our local folder. The external folder structure must remain and cannot be deleted.

Is this possible? Thanks!