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I think there is only one way a ghost fleet could realistically be in exsistence for a long period of time and un-mothballed if needed:
1. the parts used in the ghost-fleet must remain identical to those used in the normal fleet, any changes made for the normal fleet must also be implemented in the ghost-fleet.
2. the ghost fleet must not be used as a source for spares. unless the spares are soon be replaced.(to bridge the time until the spares arrive is ok)
3. any material that is rotting or deteriorating must be removed, and kept ready for reinstallation.(that means that ammo would have to be replaced in the warehouses regularly)
4. a sufficient number of trainers must be ready, always.(this should be no real problem when the vessels are identical to those still used)
5. the vessels of the fleet would have to be constructed with mothballing/unmothballing in mind, as well as long time storage.
it remains questionable wether such a "ghost fleet" still would be one, or rather a reserve-fleet.
the cost of an effective ghost fleet might be to high for it to be worthwile.
I prefer to think of it as a reserve fleet. It is perfectly possible to put old gear into storage and mothball it for future use; you don't even have to actively upgrade it. But that doesn't mean you can mothball (for example) a Star League cruiser and just leave it parked in a hidden orbit behind Jupiter for two centuries without touching it. You have to do upkeep to maintain at least a basic level of operation and readiness.
- Clean, preserve, do necessary maintenance. Start up and shut down machinery to confirm readiness, train personnel, and maintain free operation (mechanical things tend to seize when left idle too long). Replace things that expire; that includes ammo, fuel, food, and mechanical consumables such as lubricants or valve packing (a constant task on real naval ships).
- Doing the above means maintaining a supply of parts, many of which will have their own expiration dates. Fortunately, many consumables (ammo being one big exception) tend to be common and maybe not even mil spec; in reality, I can go to any hardware store and get O-rings, WOG valves, and many other basic items that will work just fine on US Navy ships today, even the ones that are decades old. But you will still have to make new ammo to replace the old, and potentially replace other old specialized equipment.
- That last need could be a good argument for upgrades, or at least replacing obsolete parts with current ones. Big E is THE example of what happens when a ship becomes outdated; most of the companies that made her original equipment in the 1950's and 1960's were long out of business before my time there in 2004-2007. When something broke, we very often couldn't get parts anymore. The solution to that is obvious: replace obsolete, out-of-production equipment, with current equipment that meets the same specs.
- Then there's the people factor. All of the above requires maintaining at least a reserve crew trained in the regular operation and maintenance of the ship. They handle the upkeep described above, and also are your experts and trainers when you have to activate and fully man the ship. At a minimum, that reserve crew should have enough people with the required skills to man stations and get the ship underway on its own in an emergency, much like a US Navy duty section. That crew needs food, quarters, gravity, duty rotation, and so forth. So either the ship's habitability must be maintained at a reasonable level, or your reserve fleet's super secret hidden base will need a supporting space station for the crews. Most likely both.
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