I think I’d go with something akin to the method used for the 2nd and 3rd retrofits (as described in 4e) and drop the original premise of replacing everything in the boltholt.
Leave the boltholes as they are and “… new caches were buried and the location was transmitted to the bolt-hole computer using references to existing cache locations.”
This retains the familiar equipment with the team as they wake and provides access to upgrades when/if they are needed. This also means a number of additional caches must be sited for each of the three upgrade cycles. Some of which could be very large if the team vehicles were part of the upgrade package. An alternative to adding cache sites could be storing the upgraded equipment and vehicles at a regional base. Then the teams could be trained on the new items when/if they find said base.
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