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Champions of Equestria

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Changelings are split into Castes, which are divided into which Changelings are fertile or sterile. Thirax and Pharynx are fertile Changelings of the Male Caste: almost all sterile Changelings are physically female due to the conditions of how the Eggs are developed, Male changelings however are virile and when they come of age are taken deep into the Hive to be protected by the Queen and Proto-Queens: tye only other fertile Changelings in the entire Hive.  
The Proto-Queens choose a Male Changeling to mate with and produce further eggs for the Hive, naturally Pharynx got action while Thorax was still too young to part-take in the process, in these days Chrysalis wasn’t Queen, she was merely a Proto-Queen the same age as Pharynx was. She loved Pharynx and chose him to be her Exclusive, and the feeling was mutual with Pharynx often referring in private to Chrysalis as “Beloved Mate” during moments of intimacy.

@Background Pony #B5EA  
Right, and I’d assume that since they have beetle themed bodies, that they instead reproduce 1-1 instead of with a hive queen.
Oddly enough, Beetles are some of the few insectoids where males and females will sometimes work together to rear young. The dung beetle comes to mind. But you don’t wanna know what happens if the parents feel that they don’t have enough food for their grubs.
Background Pony #3762
The episode explained this, just re-watch it, and accept that there not going to talk about some things.
Also Insect Queens are huge egg layers, Chrysalis was not, so she was not the egg layer, aka not there biological mother.

We need to better focus on what this species has shown since we can only go off of what is shown.
We know they start as eggs to grubs, then nymphs, and then the black soldiers. After that, they change into rainbow stags. Beetles are not normally hive type species, but can work and live together.
A detail was missed during the Feelings Forum; one changelings mentioned that “Pharynx is teaching the little changelings to be mean like him.”
That would imply one of two things; eggs/grubs/nymphs in the hive from when Chrysals’ throne was destroyed, or offspring of the current grouping of changelings.
We already know Chrysalis self imposed her rule over the changelings, and only through threats of harm did she keep her rule. She had no “hive mind” to them or any manner to make them obey beyond that. This would give credit to the idea of chrysalis knowing about what the species could do and stealing away an entire batch to groom into soldiers for her own gains.
Duck - Likes to sockpuppet for drama
Duck - 1104243, just... 1104243
My Little Pony - 1992 Edition

Your argument is structurally valid, but your premises all rest on a multitude of assumptions. The best hypotheses are said to be the ones that rely on the fewest assumptions, and I fail to see how Chrysalis being the mother of all changelings relies on less assumptions then all changelings being able to reproduce. Real world biology does not apply in a world of magical talking multicolored ponies, so it cannot be used to draw any definitive conclusions, especially when said conclusions rest on the tentative premise that changelings are exactly like real world insects solely on the bases that changelings are insectoid in appearance.
Non-Fungible Trixie -
My Little Pony - 1992 Edition

Lurking Changeling
Changelings are insects, and it’s confirmed they live in hives. An insect hive is led by one queen, who is reponsible for laying eggs. So, yes, all Changelings are Chrysalis’ children. However, this would mean that, in such a case, the term “brother” won’t mean the same thing to them as it would mean to us.
Wallet After Summer Sale -
Not a Llama - Happy April Fools Day!
The End wasn't The End - Found a new home after the great exodus of 2012

Pretty soft for a Sony.
I’m sure this episode will only further Thorax and Spike shipping… So why the hell not? Let’s marry the two and make Thorax the new Changeling Queen and Spike as the new Changeling King!
Magic Man

Fair enough then, but if that means Chrysalis is indeed their collective mother, that raises a question: who’s doing the breeding now? Or have, since the great transformation, their biology changed so they now reproduce like mammals?
If that’s what they do now, it’s gonna be pretty awkward for the current generation, isn’t it?
Background Pony #8809
They pointed this out in the episode though, Thorax said something about the eggs I think?