if we removed the skim coat and repoured a new layer would this not also need maintenance as well? Hence, it was not maintained before I purchased the house and possible the reason that it is in such bad shape having only been refaced 4 years ago...
If I am seeing this right, #1 is your overlay and #2 is your actual driveway.
Remove the overlay completely, then thoroughly clean the driveway. The epoxy stone does not need any additional overlay, other than itself. (there is no other overlay maintenance)
The pebble stone is mixed with the epoxy resin, then poured onto the driveway (we did 35sf at a time) and hand trowelled. The excess epoxy in the mixture migrates to the driveway surface and forms the bond. Some installers prefer to also roll on a coat of epoxy prior to pouring the mixture, but I've found this messy and unnecessary.
The epoxy needs a temp of about 60F in order to be workable and allow it to migrate to the driveway surface. In colder weather we're able to manipulate this a bit by heating the epoxy, but that can only overcome so much. I'd advise against installation in temps below 45F and that's pushing it. Doing otherwise and you'll see the epoxy stone delaminate and fail.
To get a leg up on maintenance, I'd advise your first reseal after year one. It's not necessary but the best long term success I've seen was done this way. Powerwash (lightly, my 3800psi can remove stone when right up on it) and roll a mixture of the same epoxy over the clean and dry surface. After that you've likely got another 4-5 years before it needs any more. Keep up on powerwashing, once a year is fine, to avoid accumulation in the areas between the pebbles.
You can reseal yourself, it's not hard, but does take some finesse. You'll have a limited amount of work time with the epoxy. Straight epoxy (not mixed with rock) can set up in about 15 minutes on a hot day (90F+) whereas you've got about 30 minutes when it's in the 70s. It might be worth it to hire this out to the installers the first time, just watch and learn. You can buy the epoxy from them the next time. DO NOT buy any of the reseal junk at a box store or paint store, it is not intended for epoxy stone regardless of what the label says.
How long is your HOA giving you to get this done? Late March is usually the soonest I've been able to begin installations, other than the occasional fluke warm day (I did one on Jan 3rd one year).