Yes it would, ...probably.
A lich Rejuvenation ability is triggered when the lich is destroyed. The petrification condition states that a petrified creature is incapacitated and transformed to stone, but not destroyed. So, if you manage to petrify a lich, it will become a statue and until it is de-stoned... or someone smashes it into pieces. A petrified lich is a really resilient statue, retaining all the lich damage inmunities and hit points and gaining resistance to all damage to boot, but it can still be destroyed with magic weapons, spells, acid, etc. All it takes is one or more well prepared minions infiltrating your garden at nigth to destroy the lich, enabling it to use its trademark escape clause and return later to enact a carefully planned revenge. Be sure to keep the statue well-watched and take advantage of the lich state to find and destroy its phylactery.
Also, if the lich happens to have the phylactery on its person when petrified (not very probable), the item will become lodged into the stone (being a magic item spares it from petrification) and you'll have an interesting choice: Leave it as it is, and hope that nobody breaks the statue, or try to extract the phylactery from the statue without breaking it yourself. If you choose the later and worst come to worst, you will have 1D10 days to find a way to destroy the phylactery (not an easy task) or to prepare for a rematch with a angry lich after its new body reforms next to the phylactery.
The designers admit the table's unclear
The first sentence in the spell prismatic wall's Effect of Color column occurs to effects from beyond the wall attempting to pass through the wall, while the second sentence in the Effect of Color column occurs to a creature itself when it attempts to pass through the wall. (The same applies to the spell prismatic sphere, too.)
Hence a creature with spells cast on it keeps those spells after penetrating the wall's sixth indigo layer much like, for example, the creature keeps its mundane ranged weapons after penetrating the first red layer and keeps its breath weapon after penetrating the wall's fourth green layer. The sixth, first, and fourth layers stop, respectively, spells, mundane ranged attacks, and breath weapons from beyond the wall from penetrating the wall; those layers don't also affect in those first sentences' ways a creature attempting to pass through the prismatic wall!
Pathfinder creative director James Jacobs in a 2010 Paizo messageboard post says
Objects, in this [prismatic wall] case, refers to nonmagical non-living things that are used to try to breach the wall. Like thrown rocks, thrown tables, arrows, catapult boulders, and so on. Any objects or items or whatever that are "attended" (as in, carried or worn by a creature) are NOT destroyed, but travel with the person carrying/holding them off to whatever other plane that person ends up going to. If the person makes their Will save to avoid being sent to another plane, he can stroll right on through the wall with all his stuff intact.
Allowing prismatic wall to automatically destroy every object that passes through it, in other words, IS a bit excessive. The intent of the spell is to prevent anyone from making ranged attacks with weapons or spells or abilities against those on he other side, basically, not to provide a static disintegration wall. The limitations of the table format forced us to be a bit more brief than we should have been in describing it, alas.
Artifacts can't be destroyed by a prismatic wall unless the Destruction line of the artifact says otherwise.
Thus the prismatic wall's layers have "their effects on creatures trying to attack you [with effects from beyond the prismatic wall] or [on creatures that] pass through the wall[, respectively]." However, this reader had to add all that bracketed information because, as Jacobs says, "The limitations of the table format forced us to be a bit more brief than we should have been in describing it, alas." (And that alas dates back to, like, at least the 2003 D&D 3.5e's description of the spell prismatic wall.)
For example, a typical creature that attempts to pass through the wall is dealt between 70 and 140 points of damage, and must make saving throws to avoid being poisoned, petrified, driven insane, and being sent to another plane, but the creature suffers none of the layers' other effects!
The creature, when passing through the wall, does not, for example, also see its mundane and magical ranged weapons destroyed by the red and orange layers, respectively, nor does the creature scratch its breath weapon off its character sheet because of the green layer, or see its spells dispelled by the indigo layer. Those layers simply stop those attack forms when launched from beyond the wall from reaching past the wall.
In other words, spells on the creature remain intact if the creature gets through the indigo layer of the prismatic wall, but spells from beyond the wall won't affect past the wall because the indigo layer stops all spells.
Best Answer
Yes, but maybe it's an error.
The description of the spell as written does indeed say that if the indigo layer starts to, but does not succeed in, petrifying a creature, then prismatic wall ends.
But given that the other language in the spell description strongly implies that that the only way to end the spell is by successively bringing down each of the seven layers, that seems really incongruous.
So, here's a theory. Suppose that in an earlier draft of the spell, the indigo layer's effects read something like this:
At some point, someone realizes that flesh to stone requires a Constitution save, which is inconsistent with the other Dexterity saves that the wall requires. So the indigo layer's effects are spelled out by copy-pasting in text from flesh to stone:
This is nearly identical to the printed effects of the indigo layer of prismatic wall, in particular the contentious the spell ends wording.
I suspect that instead of the the spell ends, what is meant here is the creature is no longer restrained. Because there actually isn't any phrase the description of prismatic wall that specifies how long the affected creature is restrained for. Compare to other spells which impose the restrained condition:
Imprisionment:
Web
And, indeed, prismatic wall already imposes another condition, and it specifies a duration for that:
But the most compelling reason to think that the spell ends is a copy/paste error is the text for the related spell prismatic spray. The effects for the indigo ray of that spell use the same language:
But prismatic spray has a duration of Instantaneous; it's already ended by the time the target is making a third saving throw. The phrase the spell ends has no real meaning in the context of an instantaneous spell.
So, my contention is that the intent of the effects for prismatic wall is that saving three times against the effects of the indigo layer means that the restrained condition on the creature is ended, but the prismatic wall is not dispelled.