If this is really one ticket, with only one ticket number, you should be fine. You would be protected in case of irrops, baggage will be checked through and of course they will see your connection at check-in in LIN. Miles and status depends on who is operating the flight, your flight number (codeshare or not), the program you want to credit to and so on. But the crucial part is one ticket. Not one PNR, not one booking, it needs to be one ticket with one ticket number.