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In combat today we were facing a medium mud elemental and it used earth glide to disappear from view (go underground). I had long arm so my reach was 10 feet. I readied an action to attack it as soon at it reappeared within my reach.
It popped up and entered into my area which set off my readied action.
At this point it then moves towards me to attack. Am I flat-footed to it at this point? This is important because AOOs cant be made when flat-footed unless you have combat reflexes.
Unless a creature is later affected by a specific effect that renders it flat-footed, as soon as a creature's had the chance to act during an encounter (typically by taking its turn when it's allowed to on its initiative count), the creature is no longer flat-footed and remains not flat-footed until the encounter ends. The disappearance of an enemy (or of all enemies!) does not instantly return the creature to its beginning-of-encounter-before-its-initiative-count flat-footed condition. For example, the typical dragonslayer won't lower his guard just because the flying dragon whipped around a nearby hill!
In short, in this scenario, since the creature that readied must have had a chance to act during the encounter previously—else the creature wouldn't've been able to take the action ready!—, the ready action should've triggered upon the mud elemental's appearance within the creature's threatened area if the creature that took the action ready picked Attack the freakin' mud elemental as the action and If the slimeball appears where I can hit it as the trigger.
As no rules govern precisely when an encounter ends, I've found that it's usually the GM who determines when an encounter ends. A GM must use this power wisely, though. Unless the GM wants the PCs using similar hit-and-run tactics, the GM should not say that an encounter ends when an enemy disappears then have that enemy that vanished 6 seconds ago gain a surprise round on the PCs.
Flat-Footed: At the start of a battle, before you have had a chance to act (specifically, before your first regular turn in the initiative order), you are flat-footed. You can't use your Dexterity bonus to AC (if any) while flat-footed. Barbarians and rogues of high enough level have the uncanny dodge extraordinary ability, which means that they cannot be caught flat-footed. Characters with uncanny dodge retain their Dexterity bonus to their AC and can make attacks of opportunity before they have acted in the first round of combat. A flat-footed character can't make attacks of opportunity, unless he has the Combat Reflexes feat. (source)
It sounds like several rounds of combat passed before the elemental sank into the mud. As long as you got at least one regular turn before readying your attack action, which you very probably did, and as long as this is the same combat, you are not flat-footed. It sounds like you might be confusing flat-footed-ness with being surprised or otherwise 'unable to react to a blow'.
Sometimes you can’t use your Dexterity bonus (if you have one). If you can’t react to a blow, you can’t use your Dexterity bonus to AC. If you don’t have a Dexterity bonus, your AC does not change. (source)
It's up to your GM to decide when you can and can't 'react to a blow'. Regardless, losing your Dexterity bonus to AC is not the same as being flat-footed and does not mean you also will be unable to make attacks of opportunity.
