You (atm at least) don't instantly lose routes. There are two choices (which are very clear in ep4) where game counts towards losing certain routes, but even those choices aren't instant route enders ^^. More like "do something like that again and it will probably end their route next time".
Ehhhhhhhhhhh I meaaaaan kiiiiinda? 😅
The "death flags" are easy to spot. As in "girl tries to kiss you and you say no" styles of flags. The other part, having enough relationship points is another topic, but so far I've been very generous with them and there isn't stuff that's locked behind "need 100% of all points" or anything similar. As long as you start focusing that girl more and more in later updates, you're fine.