The surest way to resolve this is to create a fresh Photos Library by following these steps:

1. ⌘ cmd-Q out of Photos.
2. Go into  → System Preferences → iCloud → Photos Options… and uncheck iCloud Photo Library.
3. Reboot if you want to be safe, though it shouldn’t be necessary.
4. Launch Photos with ⌥ opt-click.
5. Click Create New… and name your new Photos Library.
6. Go into Photos → Preferences → General and click Use as System Photo Library.
7. Go into Photos → Preferences → iCloud and check iCloud Photo Library.
8. Wait for your photos to be redownloaded from iCloud.

If you’d rather try to keep your existing Photos Library, follow these steps instead:

1. ⌘ cmd-Q out of Photos.
2. Create a backup of your Photos Library.photoslibrary file.
3. Launch Photos with ⌘ cmd-⌥ opt-click.
4. Click Repair.
5. Wait for macOS to repair your Photos Library. A full sync should take place once the repair has completed.

Some screenshots courtesy of OS X Daily.

Note that iCloud.com/#photos is not the same thing as My Photo Stream, and photos that were only in My Photo Stream will not appear in iCloud.com/#photos. (Unless you turn on iCloud Photo Library and sync a Mac Photos library that contains the photos downloaded from My Photo Stream, which would then be uploaded to iCloud Photo Library.) So even though the photos were still in My Photo Stream, it would be expected that they would not appear on iCloud.com.

Deleting from My Photo Stream was, at least for a while, pretty buggy. And, at least when the feature was first made available (remember deleting was not available when My Photo Stream itself launched), "deleting" photos from it meant they were only erased from the device you were using at that moment and not actually removed from the stream.

Also note the following from Apple:

After you delete a photo [from My Photo Stream], you might still see it on your iOS devices if it's more than 30 days old and you have fewer than 1000 photos in My Photo Stream.