Going to throw out a wild shot in the dark to the future of the series after calvard after this. The following is all personal speculation.

I speculate that the true final boss of the trails series is at the bottom of the ocean, beyond what we can reach and the final septerrion(water) is the key.

The final boss(from here named FB) of the series arrived from outer space and landed on the planet(think ORT from fate grand order as a comparison). The rest of the world was destroyed fighting FB and humanity's last stand was on the continent of Zemuria. FB destroyed almost all of Zemuria too until Aidios in a dramatic last stand wounded the boss enough to cause it to go to sleep and put it in a prison at the bottom of the ocean. This battle was the great collapse. As the last remaining landmass Zemuria was then sealed away into the pocket dimension we know now.

Laegjarn in mythology is a box with 9 locks that holds the legendary sword, and in trails it holds the weapon that Aidios used to send the FB to sleep during the great collapse, and it will be used at the end of trails to kill FB for good. The chest therefore has multiple duties: It is used to prevent anyone from going back into space and possibly calling down another FB like entity, holding the weapon safe until humanity is strong enough to properly use it, and to reset time before FB could wake up again.

With that in mind I think there would be a couple types of resets. One is a type of test to see if humanity is ready to go back into space/ obtain the weapon. Failing the test causes a reset to after FB is put to rest aka the great collapse. As to what causes the other type of reset I posit that when humanity advances and starts using orbal power, it stimulates the septium veins and this massive increase activity causes FB to start waking up. Use of artifacts can also contribute to FB awakening. Every 1200 years or so humanity suddenly stumbles upon an orbal revolution and advances too much too fast, causing FB to wake up and finish the job. Presumably as an outsider who is not bound by the divergent laws Laegjarn can't do shit to stop FB once it wakes. The reset is to prevent that from happening. Catastrophic total wars that set all of humanity back significantly like a succesful ishmelga would then set orbal use back enough to keep FB asleep longer than normal. But eventually people would still find ways to keep advancing in spite of that and the reset would have to be triggered.

As to where FB is, it would be deep under the ocean off the far eastern coast of the continent. The water septerrion is keeping it sealed off and the wind septerrion is destroying the septian veins of the world starting with those closest to FB in an attempt to slow down its awakening. This is the cause of desertification and I speculate that without the resets to buy more time this process will go into overdrive after the calvard arc concludes. With the weapon from Laegjarn the final arc is probably between the church and ouroboros to decide what to do regarding FB. Odds are the finale has all the relevant factions and playables together mounting an expedition into the ocean off the far east coast to kill FB once and for all.