In the four that I have in rotation, the one 2600 performs no differently than the three 2800s.

Ken

Any setting changes needed other than the charger?

None  The 2600 has enough "head room", the 2800 has more.  I don't make any changes to the charger either.
On my charger a LiIon will charge just fine using the Lipo setting.  I get a slightly smaller charge before it stops but is well over what I need.  Makes it simpler when you have both.

Ken

Ken, OP was asking the difference between 2600mah Li-ion and 2800mah Lipos.  You are comparing 2 Li-ion batteries.

As usual you are exactly right.  The answer is similar.  The LiIon will "sag" a bit sooner than a Lipo but they can be run down considerably more than the Lipo and the timer makes them pretty equal.  The Lipo should be > 20% "head room" where as the LiIon will probably be < 10%.

Ken
 

Looking at the 6S 2600 Mah Li-on battery packs in the classifieds I was wondering, are these a direct plug and play replacement for 6S 2800 mah Lippo batteries.

Six Molicel P30Bs replaced Thunder Power 6s 2800s just fine in my 68-oz. (now 67-oz.(BFD)) airplane.

 Side note. I landed today after a pattern in about 5mph wind with the timer set to 5:25 min.  The battery checker read an average of 3.45 volts on a 6s 2800 pack and I used an astounding 2718ma for the flight.  It was hot and so was the battery but the flight was normal and strong in the clover.  With a strong overhead boost setting I suspect that I was hitting 3.0 in bursts.  The plane - 60oz, 625sq", BA3514-710, 5.1 laps on 68' lines.

It is time to start making P30b packs. - Ken

Folks say you should reduce the low-voltage cutoff in the ESC.  Voltage drops more during a flight with a Li-Ion battery than with a LiPo.

Exactly, that is also reason why the LiIon combo needs MORE voltage head room than compared LiPo. Wheather LiIon can replace the LiPo in particular setup is question of that volatge head room. Motor will need pull hard when pulling nose up, so lower voltage can limit that boost. If there is enough head room it will be covered, if there is not enough, especially on end of the flight, it will loose speed. This problem is magnified by string sensitivity  of active timers. Solution is motor with more KV but it will also need more amperes.

In any case, LiIon 6s battery has end voltage like 5S Lipo battery, so it will always run at lower efficiency, fortunately it has more capacity.