Leg sorry but having some brand new shiny ships survive the war is a very likely probability. One thing the canon authors werent were naval experts (read the battle description in Satellite Down and you pretty much can see that immediately) and they really focused more on the army aspects of the war and not the naval - except Frank Frey who showed that yes the USN would still have surviving ships and an effective force where they had oil to keep them going.
And the Russian sub force basically got taken out - Last Submarine was very clear there - by mid-1997. If there had been more Soviet subs I highly doubt that the sub in Boomer would have been out there all by herself - i.e. Russian doctrine was that boomers got escorted if at all possible by other subs.
Most likely the newer ships were part of the escort for the Omega convoy and the convoy that took the reinforcements to the Middle East at the end of 2000. There is a very good chance they survived the war for the simple fact that I dont see either the Soviets or the Americans risking what few ships they had left after the huge losses in 1996 and 1997 - think the Japanese fleet in 1943 after they pulled out of Guadalcanal. Both sides probably conserved what they had as much as possible.
Also keep in mind that just because ships werent mentioned doesnt mean much in the canon - outside of the ships detailed by Frank in the Middle East and the ships in Satellite Down there are what - maybe a half dozen actual ships mentioned in the whole canon?
Also if the canon authors could forget or miss things like the 173rd Airborne or Sheridan tanks as part of the units in CA or Iran or the M88 tank recovery vehicle or the OPFOR units in CA then having those authors missing a few new ships joining up with the USN is pretty understandable.
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