You will have to reset the local variables of the character. There is no unified "undo quest x" command, as they are basically just a bunch of variables.
Thanks for the hint, I was able to figure out how to change kill counts, reputation values and quest statuses. It took a bit of digging, but eventually it paid off. This is how kill counts and reputation values can be set, in case someone else is wondering the same thing. The clues were found in _defines.fos file.
Kills:
`param 0 260 3
--> Kills: 3 men
260 Men
261 Women
262 Children
263 Super Mutants
264 Ghouls
265 Brahmin
266 Radscorpions
267 Rats
268 Floaters
269 Centaurs
270 Robots
271 Dogs
272 Manti
273 DeathClaws
274 Plants
275 Geckos
276 Aliens
277 Giant Ants
278 Big Bad Boss
279 Desert Stalkers
280 Venus Man Traps
281 Rad Toads
282 Thornslingers
283 Pashtshuurs
Reputation:
`param 0 602 3
--> Brotherhood of Steel reputation 3
602 Brotherhood of Steel
603 The Enclave
604 The Unity
605 New California Republic
606 Citizens of Vault City
607 Raiders
608 Mordino Family
609 Slaver's Guild
610 The Slags
611 Kokoweef Mine
612 Morningstar Mine
613 Broken Hills Humans
614 Broken Hills Mutants
615 Wright Family
616 Bishop Family
617 Salvatore Family
618 NCR Rangers
619 Vortis' Slavers
620 Communists
621 Tanker Vagrants
622 Crypts
623 Fools
624 Hub Criminals
625 Crimson Caravans
626 Far Go Traders
627 Water Merchants
628 The Heights Residents
629 Regulators
630 LA Scavengers
631 Gun Runners
632 Followers of the Apocalypse
633 Bounty Hunters
634 Free Traders
635 Guttersnipes
636 FLC
637 Slaves
638 Lara's Gang
639 Children of the Cathedral
640 New Reno Sex Workers
641 Hubologists
642 Cathedral of the Lost
643 New Reno Corsican Brothers
680 Klamath Citizens
681 Den Citizens
682 Modoc Citizens
683 Courtyard Citizens
684 Gecko Ghouls
685 Redding Citizens
686 Broken Hills Ghouls
687 Population of New Reno
688 Necropolis Ghouls
689 Junktown Citizens
690 Hub Citizens
691 LA Citizens
Changing quest statuses was a bit harder nut to crack, but this is how it can be done:
Open the correct map in Mapper and click on the NPC who gives you the quest. Make note of the number after ST_DIALOG_ID.
Open _dialogs.fos and search for the dialog number. This will reveal you the dialog name.
Open the correct dialog file in Dialog Editor and look for the name of the quest and what values it can have.
Open _vars.fos and do a search using the name of the quest in order to find out its ID number.
Now you know the quest ID and the values it can have.
Then use ~myinfo command to see your character ID.
Then use the command "~setvar tid_var master_is_npc master_id slave_id value" without quotes.
I don't know what the other parameters do, but everything seemed to work fine when I set them to 0 like this:
~setvar [quest ID] 0 [character ID] 0 [value]