A Possible Narrative
Assuming the wizard 13 can't use effects that reduce saving throws on the destroyed lich's remains (a conclusion that's not totally forgone but with which most agree), the wizard 13 instead needs to use saving throw reducing effects on the lich while the lich is still a lich, and those effects must persist until the resurrection's completed and the lich's made the saving throw against the helm. The 7th-level Clr spell resurrection [conj] (PH 272-3) has a 10-minute casting time, so any saving throw reducing effect's duration must be longer than that.
Maybe deal mental ability damage...
The spell resurrection says, in part, that "the creature is immediately restored to full hit points, vigor, and health." It's up to the DM whether this vigor and health includes healing ability damage (which is specifically not healed in its entirety by the 5th-level Clr spell raise dead [conj] (PH 268) on which the spell resurrection is based), but it's safe to assume it doesn't.
Undead creatures, while immune to a lot of stuff including ability drain, aren't immune to ability damage to their mental ability scores. But such an effect dealing mental ability damage still can't be mind-affecting nor can the effect require a Fortitude saving throw unless the effect also affects objects. This doesn't leave many choices.
- The 4th-level Diamond Mind maneuver mind strike [strike] (Tome of Battle 64) deals a creature that fails a Willpower saving throw 1d4 points of Wisdom damage. Note: A wizard can use the maneuver with a scholar ring of the Diamond Mind (ToB 149-150) (15,000 gp; 0 lbs.) after meeting the maneuver's prerequisites (perhaps with the feat Martial Study (ToB 31-2) and a novice ring of the Diamond Mind (ToB 149-150) (3,000 gp; 0 lbs.)).
- The 7th-level Drd spell rain of roses [conj] (Book of Exalted Deeds 106) for 1 round/level, in addition to other effects, deals 1d4 points of Wisdom damage to evil creatures within an 80-ft.-radius cylinder. This part of the spell has no saving throw. Note: Again, a wizard who acquires a resurrection spell should be able to acquire the spell rain of roses.
It's possible the wizard 13 won the fight against the cocky lich by engaging the lich in battle in an area from which the lich couldn't simply teleport away (see here) and employed the skill Use Magic Device and a divine scroll of rain of roses (7th-level spell at caster level 13) (2,275 gp; 0 lbs.), getting lucky on the 1d4 roll for a few rounds. (The lich might not've seen that coming.) (Reducing a creature's Wisdom to 0 through ability damage renders the creature helpless.) Such a narrative leaves the lich at the wizard's mercy, allowing the wizard to bombard the helpless lich with saving-throw-reducing spells.
...Then reduce saving throws with long-term effects...
Then—perhaps while the lich is at the wizard's mercy—the wizard casts the following spells:
- The 3rd-level Sor/Wiz spell bedevil [conj] (Champions of Ruin 29), in addition to other effects, causes the victim to suffer a −1 penalty on Willpower saving throws for 1 day/level. The spell allows no saving throw. Note: Because of its significant duration, a useful spell to have cast on lich well beforehand.
- The 4th-level Sor/Wiz spell bestow curse [necro] (PH 203), in addition to other choices, can be used to cause the victim to suffer a −4 penalty on attack rolls, saving throws, ability checks, and skill checks. Note: Curses are specifically not undone by the spells raise dead et al.
- The 8th-level Sor/Wiz spell greater bestow curse [necro] (Spell Compendium 27), in addition to other choices, can be used to cause the victim to suffer a −8 penalty on attack rolls, saving throws, ability checks, and skill checks. Note: Curses are specifically not undone by the spells raise dead et al. Although awfully close yet still a different source, this spell's penalty should stack with the penalty from the spell bestow curse; ask the DM. Note: See previous note. Also, a level 13 wizard must make a caster level check (DC 16) to employ an arcane scroll of greater bestow curse (8th-level spell at caster level 15) (3,000 gp; 0 lbs.).
...Then, finally, reduce the next saving throw
Then the wizard finishes off the lich with this:
- The 4th-level Sor/Wiz spell sword of deception [evoc] (SpC 217), in addition to other effects, causes the victim to suffer up to a −5 penalty on its next saving throw.
And then the wizard casts the 7th-level Sor/Wiz spell limited wish [univ] (PH 248) to cause the lich to suffer a −7 penalty on its next saving throw.
Then the wizard destroys the lich's phylactery, destroys the lich, puts the helm of opposite alignment (4,000 gp; 3 lbs.) atop the lich's remains, and casts the spell resurrection on those remains.
From the spell rain of roses the former lich's Wisdom is 1; from the spells bedevil, bestow curse, and greater bestow curse the penalty to Willpower saving throws is −13; and from the spells sword of deception and limited wish the penalty to the lich's next saving throw is −12.
Even if the wizard defeated the lich using a method other than the spell rain of roses, that's still a −25 to the resurrected lich's next Willpower saving throw. And even if the DM says the penalty from the spell greater bestow curse isn't cumulative with the penalty from the spell bestow curse (or if it's distasteful to have the wizard use a spell from a scroll), that's still a −17 to the resurrected lich's next Willpower saving throw.
While an optimized lich may yet succeed on such a saving throw, it'll struggle mightily for that success if, in conjunction with these methods, prior to its resurrection, it's stripped of its gear and the targeted version of greater dispel magic is employed to remove any ongoing protections.
- Without knowing your lich, I looked at some other liches. Mael-Brigte Feórna is a lich (formerly human) Sor20 with Wisdom 15 and a Willpower saving throw bonus of +10. Tevangia Zail, Archmage of Lichdom, is a lich (formerly half-elf) evoker 13/archmage 5 with Wisdom 15 and a Willpower saving throw bonus of +17 (Libris Mortis 156). (Lower-level liches are easier to find; I ignored them.) While the latter lich is better designed (having, for example, a spell component pouch among her possessions), neither is particularly optimized and neither can withstand this assault to its Will save.
- Consider making a better helm of opposite alignment. The saving throw DC of 15 means its effect is equivalent to a 3rd-level spell (despite most being created at caster level 12). For example, although it appears in the Epic Level Handbook, the non-epic item creation feat Enhance Item (34) is an extremely easy way to justify a more powerful helm.