This is a tricky one, because arc fatigue can be real, and I have definitely both experienced making comics where the characters being in one place, doing one thing and facing the same problem or villain with no end in sight was causing readers to get bored reading it, and also seen other comic creators struggling with the same problem. I've definitely read comics like that.
The key isn't necessarily to not focus on these longer arcs, but to make sure that the way the longer arcs are told and drawn keeps creating visual and story interest and doesn't stay the same the whole time. So try to make sure that throughout, you keep showing the reader different things visually, by changing the environment they're in (even if it's by changing the lighting or the level of destruction in that environment) and switching which characters you're focused on, try to have the tone shift occasionally between calmer moments of discussion, bits of comic relief and intense actions or emotions, because all one tone all the time gets tiresome.
Also if you can remind the reader what they're fighing for; either what the characters' motivation is for saving this city, and/or why that's important to the wider plot, it hopefully shouldn't fall into "...why are they doing this again?"
Finally, just general good webcomic pacing is to always make sure something interesting, funny, cool or exciting happens on any given update. Avoid pages that are just characters waiting, walking places, continuing to fight without something that's either funny, uniquely and specially cool/sexy/scary or changes things with a juicy piece of lore or plot or altering the situation or stakes in some way. So long as updates feel interesting, intense or fun on their own, you can hopefully keep both the weekly readers and the binge or book readers excited!