The message did not say it deleted them but that they were disabled. No need to redownload you just have to enable Mods and CC again in Options | Other.
They were disabled because when there is an update to the Game some Mods and CC will break requiring them to be updated or removed if no update is available.
You say you did enable them again and downloaded some new CC and that didn't turn up. This is likely because you didn't place it in the right location, usually Documents\Electronic Arts\The Sims 4\Mods, or that they were in a compressed format such as zip or rar and you didn't unpack them.
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