I haven't noticed if it happened between other level improvements too, but at least when building level 5, then the youth arriving restarted from day one :'( although I had rather few days left to new players where supposed to arrive,
AND the message before I ordered the building did say it will not make anu DURING I build 3 days, DIDN'T say restart...

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An other thing concerning youth schools. 20 days is shorter than a season. Isn't it better they arrive in END of season, just before some other player's contract end, so we can chose who to sign and we will not be short of players during waiting for youth players to arrive either?
OK to let them arrive in the quality the school had when the players STARTED developing to simplify it.