I thought Lydia had died but couldn't find her corpse so I resurrected her with the command "player.placeatme 000A2C8E", creating a new instance of her. Now I have returned to Breezehome and the original Lydia is there. She has all her usual talking options, but the follower commands don't work. I can pickpocket her.

The "new" Lydia (with a ref id starting with ff) actually works fine, but I would prefer to use the "real" one anyway. Is it possible to fix her? If it is not, are there any actual disadvantage in using the cloned one (broken quests, etc.)?

Yes. Select the doppelganger Lydia after opening the console and type "disable". Never use the "placeatme" command with named NPCs. If you can't locate the one you need, look up their base ref ID on UESPWiki, use that with "prid" then use "moveto player" to bring them to you. For Lydia, that would be:

prid a2c94
moveto player

In some cases that will break dialog options (bringing a vendor out of their shop, for instance) in which case you should use, for example:

player.moveto 1a66d

which will place you next to Arcadia in her shop.

Thank you. After I followed your instructions, her follower options still didn't work, though. To fix them, I had to dismiss and re-recruit her.