I kinda agree to this, it has happened to me too, accidently walking outside and need to re-pay the 5k fee.
As for the reset timer, it's 22 hours, you should do like me, i have a notepad file with all my PRO Info, bosses and their pokemon, when i fought them and when will they be available again (date and time), what time i went in excavation, what time i did my headbutt run, when did i do my dig run and when it resets, etc.
You get the picture.