So, apparently I have -6 rep in a town, where I maybe violated curfew in once or twice.(Typically, I'm quite the goody two-shoes in RPGs) The shadiest thing I've done is smooth-talk my way past a entry toll. My best guess is that I assisted an enemy faction of theirs or something. I surrendered one time, and was brought to the dungeon, which I seemed to be stuck in forever. There's an option to "stoically wait for the Magistrate's sentence" but you need to actually do something each day before it kicks in. And even then, you can't just wait out the whole thing at once. You can dig your way out stupid fast, but it won't help your rep I assume.

Any tips? Thanks

Could'nt you also visit all the shops in hope for a quest? I believe that raises local rep as well... (if you complete it that is)

Smooth talking your way past the guards won't hurt your local rep, but sneaking past can. Running from the guards can also lower your local rep.

You've been thrown in prison? You might as well jailbreak and ditch this city. Try not to kill anyone on your way out or you will be steering clear of here for a long time to come. Alternatively, you can spend your time inside talking to the priest until the magistrate sees you, but that path isn't recommended.

If this city is part of a princedom/governorship, you can try sucking up to the prince in one of his other cities. You might find that you start off with negative rep there too, but it shouldn't be as bad as it is here. Unfortunately, the prince won't see you unless your reputation is high enough to get past the clerk, so you'll probably have to move on and come back later if you need something from this city.

Doing good deeds in the nearby countryside can also help your local rep. Killing brigands or nearby raubritters, for example. Helping travellers.

Later on, you can get saints who boost your local rep, which should solve most of your low reputation issues. Unless that saint is only available in the city you're barred from. I think there was more than one saint, and there are other places where you can learn saints.

Europe is big. Losing one little city won't hurt you much. Unless it's an important city with a university or cathedral or good stores like Nurnberg, then yeah, that's going to hurt until you fix it.

I'm having a similar issue, except I did my time, and managed to even check my reputation before entering several cities, and it was either low (4) or decent (16 or 18) and I am STILL getting arrested. Is there a way to check your regional wanted level, or something? I've had to essentially restart with no items twice due to this.

Are you being arrested on sight?
Certain actions will get you arrested even if you have a positive reputation in the town, but you shouldn't be getting arrested without provocation.

One of the best things you can do if you need to start from scratch is go back and forth between the shady grove and the side streets. You'll run into bandits a lot and the night watch very rarely. The bandits are pretty easy and selling all their drops will get you some decent gear plus improve your reputation making it cheaper to heal back up at the inn.

If the night watch catches you, try talking your way out of it first. It will sometimes work but even if it doesn't, your skill may still improve. If you fail, always pay, it's not that much and your reputation won't suffer.

Odd ways that local rep gets lowered: wake up craftsmen, clothiers/dyers at night to make a purchase, kill a bishop or noble's party overland (nearest city gets angered).

Successfully talking your way out of the gate toll increases your local rep. Apparently guards are people too and if they like you, that counts for local reputation. I've managed to become "local heroes" in a town simply by talking my way out of paying tolls about 30 times...

@OthelloNYC
The only way I'm sure you could get a warrant with a positive local rep is by seeking sanctuary. Is that what you did?

I literally just entered the city through the front gate and was arrested on sight. This happened three different times, and in all three cities I had a positive reputation, but it was after I narrowly avoided execution with a miracle and then took sanctuary in a different city. I was curious if maybe it was because the region reputation overrode the city reputation.

Once you get to a certain local reputation (which i'm fairly sure is -5) then you activate the 'wanted' flag for that city. this flag stays even after you increase your reputaion again. Unfortunatly, there is no in game way of removing this status, you could work your way up to Local Heroes only to have the guards arrest you anway.

Some cities are part of a Kingdom, Duchy, Palatinate etc. When you approach the city it will tell you who is in charge of the city and if they are running it on behalf of a higher noble, actions that cause a wanted status in one of these cities wll affect all of them.

WIthout reloading or restarting the best thing to do is just avoid those cites, as other posters have said Greater Germany is large enough that losing a few won't hurt your long term prospects.

Think of it as a role playing opportunity, your young party was framed for a crime they didn't commit and had to flee the area for their lives vowing to return one day get revenge on the corrupt Prince/Mayor/Guard Captian etc.

I've been there and after day's of waiting preying for penance and trying to dig my way our with a spoon. I was executed I think I may have tried to fight the guards as I had no money to pay them off. I though I draw swords and run. thought it worked but was arrested soon after. I think with some saintly Aid you can get rid of the wanted status. I had a lot of experience. When I first started playing I didn't realize that I could just walk out the gate's
Does make for an interesting time.
I used to fight those pompous Traveling clergymen you know the one's with the Knight's. they would get not 1 Phenning from me. I think I had a negative rating of 25 or 30 once. all the surrounding cities were after me
I had to sneak in every city lucky I had a Saint to help with that. don't remember how long I lived but I was eventually capture and my head was freed from my neck . good times