I performed these instructions below, and I still have the same problem. The progress from my desktop Anki is not updated onto my AnkiWeb.
After this process I didn’t lose the cards in my desktop, but I lost all my progress. Meanwhile, the AnkiWeb cards were not updated with the ones from my PC.
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Because the first sync can only sync changes in one direction, if you have added different content to different devices or profiles before setting syncing up, content on one device will be lost if you overwrite it with the content from the other device. With some work, it is possible to manually merge data into a single collection.
Start by taking a backup on each device/profile, in case something goes wrong. With the computer version you can use File>Export to export “all decks” with scheduling information and media files included, and save the file somewhere safe. In AnkiMobile, the Add/Export button on the decks list screen will let you export all decks with media.
Next, if one of your devices is a mobile device, synchronize it first. If there’s a conflict, choose “upload” to overwrite any existing data on AnkiWeb with the data from your mobile device. If both devices/profiles are on your computer, synchronize the device/profile with the most number of decks first.
Now return to the other device/profile. If automatic syncing is enabled, a message may pop up asking if you want to upload or download. Click the cancel button - we don’t want to sync yet.
Once you’re looking at the deck list, click the cog icon next to the first deck, and choose “export”. Export the content with scheduling information and media included, and save the .apkg file somewhere. Now you’ll need to repeat this for each top-level deck.
Once all top-level decks have been exported, click the sync button at the top right, and choose “download”, which will overwrite the local content with the content you synced from your other device.
You can now use File>Import to import the .apkg files you exported earlier, which will merge the exported content with the existing content, so everything will be in one place.