When using minor change shape, the changeling keeps any templates the changeling gains or already possesses
The changeling supernatural ability minor change shape says
Changelings have the supernatural ability to alter their appearance as though using a disguise self spell that affects their bodies but not their possessions. This ability is not an illusory effect but a minor physical alteration of a changeling’s facial features, skin color and texture, and size, within the limits described for the spell. A changeling can use this ability at will, and the alteration lasts until he changes shape again. A changeling reverts to his natural form when killed. A true seeing spell reveals his natural form. When using this ability to create a disguise, a changeling receives a +10 circumstance bonus on Disguise checks. Using this ability is a full-round action. (Races of Eberron 41 and link added)
Thus the minor change shape ability is a disguise—it's a disguise that physically changes the creature, but a disguise nonetheless—, and the changeling's disguise alters nothing about the changeling below the disguise.
The benefit of the feat Racial Emulation says
When you use your minor change shape ability to assume the form of a humanoid creature, you can also emulate any of that humanoid’s subtypes. Though you do not gain any of the humanoid’s traits, you are considered to be a member of that race for all other purposes (allowing you to use magic items or spells keyed to race, for example). You can also ignore the normal penalty on Disguise checks when disguising yourself as a different race…. You can only emulate one race at a time, and you always retain the shapechanger subtype. (100–1)
Thus the feat Racial Emulation only improves the changeling's disguise. The supernatural ability minor change shape is—as the feat says—a kind of form-changing magic, but it's a very specific kind of form-changing magic. Unlike many other ways that a creature can change form, the changeling only changes its form according to these two abilities, and these two abilities alone. So while the changeling could use the ability and feat in tandem to assume the "form" of, for example, a half-dragon half-fiend hobgoblin, the changeling would actually only have the minor physical alterations so as to appear to be a half-dragon half-fiend hobgoblin and not any of the creature's abilities. Further, while a DM may allow a changeling to assume the form of a dwarf that's undergone the Savage Species ritual of the elements so that the dwarf "form" possesses the subtype earth—certainly a stretch, by any reckoning!—, nothing else about being a dwarf will be gained—and nothing else about being a changeling will be lost—except appearance, maybe some subtypes, and what the ability and the feat detail.
That means if the changeling does somehow acquire the normally-inherited template muck creature (Advanced Bestiary (2004) 183–5) while the changeling's using the minor change shape ability, it'll keep the template muck creature no matter what form it assumes when it uses the minor change shape ability. A creature that's merely disguised—whether through physical alteration, a glamer, or Groucho glasses—can acquire a template and keeps that template no matter what disguise the creature later dons or how the creature dons it. A muck changeling remains a muck changeling even while using the ability minor change shape, a winged elf remains a winged elf when affected by a disguise self spell, and a werewolf human remains a werewolf human despite wearing Groucho glasses.
However, were the changeling to employ a more radical kind of form changing magic—like, for example, using the 2nd-level Sor/Wiz spell alter self [trans] (PH 197) to assume the form of tren—, the changeling would lose the template muck creature in that tren form as the changeling's original form is, according to spell's description, entirely subsumed into the new form that's just been assumed.