i always play w/ plane replacements/upgrades OFF, so i can control the flow of aircraft. as Allied player, you have v. limited control over production, but you can manage where the produced planes go.
if Yorktown's aggregate damage is > 50%, she can't conduct air ops, this may extend to replacements. access her airgroups from the base-hex 'show ships under repair' screen, you may be able to xfer them to the land-base at Pearl, where they'll be able to accept replacements and perform missions, if new planes & adequate supply are available. when
Yorktown is repaired, use 'transfer to ship' to fly her air-groups back onboard.
it helps to keep a side-record of which sqns belong to which ships, esp. when ships go in for lengthy upgrades/repairs. their pilots won't train while they're in the yards, xfer them to the land-base & train them!