Is there a way to allow horses to take some decay / damage but not let them be killed / despawned? Like maybe turn on decay for only a bit to let them take some decay so they will eat and then turn decay back off? From what I understand, they need to decay / take damage in order to eat and they need to eat to produce dung. None of my horses on my server eat or produce dung. I asked in the support for TruePVE and they said it would be a decay plugin causing the issue. 

You could try just turning down the decay to very low. Health is a decimal, so decay could deal something like 0.0001 damage, and that might be enough to make it eat, though I haven't tried this.

Thank you, I will try that.

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That did work! TYVM. I have the horses decaying at 0.0001 like you suggested and they are eating / pooping now.

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I just have to make sure I keep them fed since they decay now. 

If you set the decay sufficiently low, then you do not have to make sure to keep the horses fed since it would take months for them to die.

For example, at baseridableanimal.decayminutes 180 (default), a horse will die in 3 hours. At 1440, it would take one day. At, 43200, it will take one month. Multiply that to 100 and round up to 5000000, and the horse will take less than 1 damage in the course of a month.