Javelins are fine.
Defiling Rejuvenation seems good, though 6d6 seems like a lot of damage for a 4HD monster. I guess most PCs won't be plants, so it's kind of a corner case, but I'd go for a lower value.
Yes, it's only a placeholder.
My first thought was to make it 1d6 per Hit Dice, or 4d6, but then I thought the caster level should be higher than 4th so tweaked the damage up.
Upon reflection, 1d6/HD would be enough.
Charisma-based seems most appropriate, so I'll pencil that in.
Apart from that, it's just the toughness of the gem and the CL to figure out.
Should the gem have any hardness?
Caster level 4+HD would seem to fit - I'm thinking it's a strong ability. Although 2+HD would be decent too.
That reminds me - what happens when a defiling skeleton is turned? Does it have turn resistance? Does it reform if the cleric gets a "destroy" result? I'd prefer it if turning could destroy or prevent their Rejuvenation. We'd better add something in about turning, but I'm not quite sure what.
Anyhow, so far we've got:
Defiling Rejuvenation: When a defiling skeleton is reduced to 0 hp, it collapses and becomes inert for one round. The next round, it draws life-force from all vegetation within a 30-foot radius, killing all normal plants within the area. Plant creatures take
1d6 damage per hit dice the defiling skeleton possesses (DC
X Fort save for half damage). The obsidian jewel in the skeleton’s forehead glows brightly while this defiling of nearby plant life takes place. The save DC is
Charisma-based.
The next round the defiling skeleton rises up, restored to full hit points. Striking the skeleton while it is inert has no effect, nor does it delay the rejuvenating. Only the destruction of the jewel embedded in its forehead (AC
Y, hp
Z)[
AC 13, hp 6?] or the successful application of a dispelling effect such as
dispel magic or
break enchantment can stop the rejuvenation. Defiling rejuvenation is considered an
4th? level spell with a Caster Level
equal to 4 plus the skeleton's Hit Dice.