I tend to sip my coffee very slowly over the course of a day. I brew about 12~14 ounces at home, and pretty much sip on it over the next 6 hours at work in my thermos. Over the course of the day however, I notice that my brew slowly gets more bitter towards the end of the day. When I underextract just a little bit, it gets better after 1 hour, and then progressively goes bad after 3. When I get that perfect balance, it starts to go bad after 1 or 2 hours. It never gets so horrible that I'd rather not drink, but it does get noticeably worse. When I overextract a tad, forget about it. Drink it while it's hot and dump the rest later

Would anyone be able to shed some light on why this is? Should I accept this for what it is? Is there a way to brew coffee so that it stays good for hours? Is it technique? Is it grind? Inquiring mind would like to know

The Chlorogenic acid in coffee breaks down into caffeic acid and quinic acid as you hold it at temp increasing the bitterness in the brew. This is one of the reasons that many cafes enforce a time limit that they'll hold coffee at before dumping it.

I have experienced on road trips that sometimes coffee that I hold in a thermos (it was brewed in a Vac Pot so it was very hot going in) got better, with more fruit as it was held, but then got worse.

One way around this would be to brew coffee over ice and then re-heat it when you want to drink it later, or just brew coffee on demand. You could also look at how your filtering coffees, a coffee that's highly filtered may not get as bitter as quickly.

Would a chemex brew be clean enough

You could try rapidly cooling the coffee and then reheat it, makes sense, i've had better experience in taste carrying freshly brewed iced-coffee (japanese method) in a thermos for a couple of hours than with hot coffee. Reheating iced coffee sounds a bit risky, but it might work.

Other than that, i'd say no, you can't keep coffee tasting fresh for more than 20..30 minutes, coffee flavors/aromas are extremely volatile and change dramatically with exposure to oxygen and changes in temperature among other things, and it's not the just bitterness , most of the complex, delicate and yummy flavors are gone as well.

My suggestion? carry hot water in your thermos and brew the coffee at work, or adjust your drinking habits so that you only drink coffee within no more than 1h after you brewed it.