San Dorino! thats what its called. good. Yea the only problem with my second option hypothesis is that it doesnt really explain why San Dorino doesnt exist in 1000 A.D. AFTER Crono defeats Zombor on the Zenan Bridge. Crono and co. secure the Bridge for the humans and go to Denadoro mts to get the Masamune. Then they leave for awhile to get the Masamune repaired (but no mystic attack occurs in this timeframe because when the party returns to 600 A.D., San Dorino still exists). Then the party storms the castle, defeats Magus and leaves 600 A.D. for awhile again (still no mystic attack on San Dorino, everything seems hunky-dory).
Basically the game offers no obvious or easily discoverable sublte solution to why San Dorino does not exist in 1000 A.D. I can, however, think of 3 possibilities for its non existence in the altered 1000 A.D.
(1) The 'war' between the mystics and humans had been going on for quite awhile, but it was only when Magus assumed power that true war began. Perhaps San Dorino was the victim of some giant hate crime against humans by the remaining mystic extremists or perhaps it was destroyed much later by mystics from Medina for similar reasons. These situations are unlikely as they would have started another war (perhaps there was one large battle in 712 A.D. or something that wasnt mentioned in the game with the humans coming out victorious, but there just isnt any support for this possibility in the game).
(2) Remeber the Cursed Woods and Guardia Forest? Yea monsters live in forests. Perhaps with the spread of Fiona's woods, monsters or even just dangerous animals (bears, cougars, koalas) entered the town and messed with the citizens (probably children playing). The town was most likely not destroyed by these creatures, the citizens probably moved out to Porre and Truce. (Again this kinda makes sense, but the Curseed woods were close to Porre [though probably not as close as Fionas woods eventually were to San Dorino] and in 1000 A.D. forests are all around Truce. But the creatures in the Cursed woods were significantly stronger and more dangerous than the birds and beetles of the Present, so perhaps this possibility is correct.
(3) Being very close to Zenan Bridge, San Dorino either was or eventually developed an economy based on trade between Porre and Truce (perhaps they had delivery services, had inns and restaraunts for 'businessmen', had open markets for constant passerby travelers from the two towns, etc.) But with the invention of the Ferry system, travel using the old Zenan Bridge began to die down significantly as tourists, vacationers and businessmen enjoyed quick and easy travel on the ferry from Porre to Truce and vice versa. Kinda like how mom and pop stores lose business to the walmart next door, eventually the town failed and its citizens moved to Porre and Truce to take advantage of the markets in those towns or something.