You need to filter by a single set to see your owned “permanent copy”. Eg: GvG for Shieldmaiden.
Also be careful when disenchanting as your Wild copy counts as the same card in collection for Classic mode. You disenchant your Al’Akir, it is gone from Wild and Classic.
My guide here:
Disenchant extra copies of cards when they’re nerfed for lots of dust.
Get the rewards track free cards and do your quests. Gold and packs will build up over time.
You might be encountering a returning player bug, there are Bug Reports that some players lost a lot of their previous collection. I’m not sure really, because there were only a few reports and not even screenshots