I can't continue the Path of Banishment because Rachel is locked in her room crying because of what happened to her cat.
Don't worry. This problem will solve itself. Just wait a little bit...
If affection points are going to be necessary, there should be more ways to earn them than by hitting the appropriate conversation at a given time (that's for VN and this is a sandbox). In a sandbox, you are expected to be able to do something to get back the points that you haven't earned by following the story (such as entering into conversations with the LIs or helping them do things)
I personally like to be challenged in games - even in AVNs. Therefore, I use the affection system as a sort of riddle system. That's also why the quest log doesn't tell you how to get the points and why the affection points matter to cross thresholds. In many other (sandbox) AVNs similar point systems are usually insignificant for the story progression and only give you a small dopamine rush when a notification pops up.
Also, sandboxes tend to turn into grind hells, so I don't have any farmable "stats" like money. Affection points are only obtainable via non-repetitive events, to still be a sort of challenge/accomplishment. At the moment, I plan to deal with not-earned points, by adding very easily obtainable replacement points for hard-to-guess ones (Sabrina's last hit for example) in the following release.
I know this will not work forever, so I also have a vague concept for that:
Since time travel is already vaguely teased in the game, I plan to give the MC the power to alter little things in the past i.e. regain lost affection points/switch choices. At the moment, this is only a vague concept and please don't ask me for any specifics neither story-, gameplay-, or script-wise.
Otherwise, with Lintar I have -1 affection and I'm not sure if there is any way to improve it (to be honest I haven't looked much).
There are two ways to get Lintar's point for you at the moment:
With Sarle and Saefia I have proceeded to choose the options that didn't give me affection points with them, so right now I have 0 with them. I don't know if this limits anything since I haven't started the quests "Divided by Time and Space" which I suspect is a Sarle's quest, "The Oldest Contest of Civilization" which I suspect is Saefina's, and "Somebody Ate from my Plat"
Yes, "The Oldest Contest of Civilization" and "Somebody Ate from My Plate" are mainly Saefia-focused side quests, that can easily skipped/ignored. Maybe you'll lack some affection points down the road, but I'm not sure as of now... "Divided by Time and Space" starts out as a quite Sarlé focused quest, but will turn into an Annica-/Adrian-focused quest line, that will turn out to be quite important in the long run.