You shouldn't have problems checking 6 hours prior to the flight as it's their hub. If you're not gold, most luggage checking is now done using the self drop kiosks.
Just FYI, 6 hours is waaaay too long to spend at the lounge in LIS. Once you check your bags, take the metro (or grab an uber) to Oriente and walk around and enjoy some fresh air there. You can, of course, go to the city center and enjoy your time there as well.
Note - if your flight is at 6AM and you're thinking about doing this at midnight, neither the TP nor the airport-run ANA lounge is open overnight.