Eldritch tokens are often used for differing purposes and different mythos cards and effects. Can they or should they be used generically across all active effects? Here is an example.
The Cthulhu ancient one spawn Eldritch tokens on any sea space occupied by an investigator when a reckoning effect occurs and the ensuing effect is investigators traveling through these spaces get delayed (stopped in their tracks). One of the mysteries for this ancient one places Eldritch tokens on each sea space nearest each investigator and allows them to test against it and spend clues toward solving the mystery.
Does this then mean every Eldritch token, whether it was placed by the Cthulhu reckoning effect or this mystery now delays investigators, and every Eldritch token is a candidate for being tested against to progress through the mystery, or do we have to have some way to keep track of which tokens were placed by which mystery/effect? I can see either approach as being easier or harder in both cases, so using the "harder on investigators" reasoning doesn't work. The sensible storyline approach argues that the tokens should be unique to the mystery/effect that created them.
I lean toward the sensible story approach but it is rather fantastic to consider that so much is going on in this wild flurry of activity that maybe it is worth simply saying an Eldritch token is simply indistinguishable from any other token once it's placed.
Update: The reference guide indicates that
When the active Mystery is solved or removed from play, discard all tokens on it or placed by it. Then draw a new Mystery, placing it on top of any solved Mysteries.
so at least there is some maintenance of the eldritch tokens (pulling them off) as these get solved. I do not know if mythos cards result in eldritch tokens being placed in locations.