Frankly, an out of universe answer may be most applicable here.
With few exceptions, in terms of actual in-universe consistency (barring Stardates of course) you can generally watch TOS episodes in any order. The thing to remember with TOS is that it wasn't intended to maintain an arc or generally even minute consistency from one episode to the next (except in broader beats). It has been said that TOS has no memory from episode to episode - unlike later series, TOS was meant to be an anthology show or little morality tales set with the same characters and settings. Additionally, apart from production staff like Robert Justman, Dorthy Fontana, Gene Coon, and Roddenberry polishing and modifying scripts, each episode had different writers that may not have been familiar with previous episodes. Scripts were often selected as to what to produce and air next, not on a story basis but in terms of time and cost and simply if the script was ready to go or not.
TL:DR - because Jerome Bixby (story for By Any Other Name) didn't write the next story (Return to Tomorrow - John T. Dugan) and nobody bothered to worry about what happened in the previous episodes generally from a broader, overarching storyline perspective
- source: paraphrasing and analysis from reading Marc Cushman's "These Are the Voyages, Series 1 and Series 2 production background books)