How Dungeons & Dragons, Third Edition can permit in the Forgotten Realms the epic feats Improved Spell Capacity (Dungeon Master's Guide 210) and Epic Spellcasting (Epic Level Handbook 55) despite that setting's ban on high-level spells due to Karsus's Folly is detailed in Lost Empires of Faerûn (2005) on Mystra’s Ban and Epic Magic:
All those who live by magic know that in ages long past, mages had access to spells of great power. In the aftermath of Netheril’s fall, however, Mystra banned certain high-level spells that she deemed too powerful for mortals to wield responsibly. Thus, current-day spellcasters no longer have access to true spells of 10th level and higher. Instead, access to epic magic comes via two feats—Improved Spellcasting Capacity and Epic Spellcasting—that function in very different ways.
The Improved Spellcasting Capacity feat grants spell slots above 9th, theoretically without limit. Before Mystra’s ban, powerful mages could fill these spell slots either with true spells of 10th level or higher, or with 9th-level or lower spells fortified by various metamagic feats. After Mystra’s ban, only the latter option remained available.
The Epic Spellcasting feat allows the development and casting of epic spells (spells requiring the use of the epic spell system presented in the Epic Level Handbook, cast through superior mastery of the Spellcraft skill). Mystra’s ban has never applied to epic spells, even those that duplicate the effects of 10th-level and higher spells developed before the fall of Netheril.
Epic spells did exist during the days of Netheril, but the Netherese largely abandoned their development after the discovery of the nether scrolls. During the age of Netheril, epic spells were largely the province of the Fair Folk and were thus almost exclusively associated with elven high magic. The Netherese, for their part, preferred to develop and use 10th-level and higher spells. (43)
Thus, because the feat Improved Spell Capacity doesn't allow casting true 10th-level or higher spells and only 9th-level and lower spells modified by metamagic feats, the feat's benefit doesn't violate the ban. (Even spells that have been modified by the epic feat Improved Heighten Spell (EL 58) don't technically make a spell an actual, brand new, unique spell of the new spell level even if the spell's effective spell level is increased to higher than 9th level.)
Further, to read between the lines, while 10th-level spells existed in Second Edition (the Wizard's Spell Compendium details them, for instance), epic spellcasting as a concept is unique to Third Edition, not existing when the ban was initially formulated (see this question), making it so it's only a minor retcon to say the ban never applied to epic spells in the first place.