I had made a deck of cards on my iPad and synced them with Ankiweb. While syncing my Ankidroid later, I found that the new cards haven’t come on Ankidroid. I checked the same on Anki Windows but the new decks there also wasn’t synced. So again I synced my iPad Anki app and two recent decks got deleted. I was able to retrieve one from backup but had to again make the other deck for an hour 
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Hmm, that’s odd - I can’t think of any reason why that would happen if you didn’t do a full sync. I suggest we keep an eye on it and see if happens again - if it does, I’d recommend you export your collection before attempting further syncs, so you’ll have an immediate backup to restore to.
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If I create a backup from settings, does that include the media files ?
Backups skip media - you can include media if you use the export option instead, but since existing media is preserved when importing a backup, it’s usually not necessary.
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Hey, the same old issue happened with me too, didn’t lose a lot of cards but want to make sure that it doesn’t happen in the future. I have started using the app recently and would love to get some help.
Please see Syncing with AnkiWeb - Anki Manual