Sorry, cannot make heads or tails of this. Sorry. The following is my best guess...

I have created a song/mixing and have 6 parts transmitting to channel one to create splits and layers.

Forgive me, but no you haven't. Parts do not transmit, Parts Receive. So it is likely you meant to say, "I have 6 Parts set to receive on MIDI channel 1" At least that's what I hope you mean. The keyboard transmits, the Parts receive. You are playing (transmitting) via the keyboard and have six Parts set to receive on channel 1 (my guess, but not at all what you wrote).

On ch 6 I have a voice that I have added an arp to and only want the arp on that one voice.

I thought the six Parts are on channel 1 so you've lost me. Unless now you meant to say "Part 6 is assigned to play an arpeggio" in which case, fine.

When I direct ch6 to transmit to ch1 the ARP effects the entire keyboard.

How can ch6 be directed to play ch1? You've lost me again. Your understanding of MIDI transmit and MIDI Receive needs work!

I have tried setting a L/H limit in arp edit but this effects how the arp sounds. Please advise!!!

I would ask you to please try again and provide what you would like to accomplish.

My guess:
Performance mode allows you to create four Part setups. You can Play and Record directly from Performance mode using the direct Performance Record feature.

If you are attempting to "cheat" this rule and use a Song/Mixing setup to include more than four Parts, you can, BUT, you will not be able to Record - if that's what your trying to do, it will not work.

You say the Arp is triggering all Parts, again, forgive me, no its not... in fact, the Arp is triggering only Part 6.... everything should play fine. unless you are trying to "Record". You can't! Recording multiple Parts simultaneously is not possible via this method. You can perform it live, but obviously transmitting all of this on the same MIDI Channel and trying to Record it chaos ensues... everything on the MIDI channel response. It has no choice.