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If I'm not mistaken, last two seasons of Star Trek The Next Generation were aired in parallel with first two seasons of Star Trek Deep Space Nice, and most of the episodes in both series had their stardates matched. Are there any remarks to issues mentioned in ST:TNG "Force of Nature" (possible destruction of space fabrics by using warp drives) ever addressed or at least mentioned in Star Trek Deep Space Nine?

From what I saw so far (just starting DS9 season IV) there is no such thing. We have a strict declaration in "Force of Nature", that under no circumstances, except for an extremely dangerous situations, no Federation ship can speed more than warp 5. Yet, we have many clear examples in DS9 in season II and III, where we can see Defiant speeding at warp 8 or so in situations, which barely can be taken as extremely dangerous.

Is there any in-universe explanation for this "glitch"? Or is there something, that I don't follow and there is nothing to explain here, as there is no "glitch"?

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    The implication from later episodes is that the Federation have retooled their engines to deal with the issue, first by using variable geometry engines (like Voyager's), then by redesigning their engines to simply remove the problem. We can assume that this info was shared to the other regional powers all of whom would have a vested interest in not damaging subspace. – Valorum Dec 19 '15 at 14:55
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The short answer is that it's not addressed again, beyond the end of TNG.

In-universe explanation

Quoting from the Star Trek Encyclopedia (2nd Edition)

The council further ordered Federation ships throughout the galaxy to restrict their maximum speed to warp 4.7. (TNG: Force of Nature). The Starship Enterprise-D and other ships observed the "warp speed limit" for the remainder of Star Trek: The Next Generation. After that, it was assumed that Starfleet was able to develop a more "environmentally friendly" warp drive, so the speed limit was evidently lifted.

One can assume that if the fix was actually quite trivial, the other major powers would have had no qualms about enacting it.

Out of Universe explanation

As to why the decision was made to simply gloss over the problem, the simplest way to look at it is that continuing to insist upon 'warp-speed restrictions' would have demanded regular explanation (adding to the length of scripts) without actually improving them in any way.

As Ronald D. Moore stated in the Captains' Logs: The Unauthorized Complete Trek Voyages book:

...when you limit warp drive, the rug is being pulled out from under Star Trek.

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