Jordan Petridis commented:
People report that it started happening again
https://paste.gnome.org/pfjfeompn
$ flatpak install org.gnome.Sdk/x86_64/master --reinstall --verbose --ostree-verbose --user -y
F: Opening user flatpak installation at path /home/ivans/.local/share/flatpak
Looking for matches…
F: Fetching summary file for remote ‘flathub’
F: Adding GPG keyring data from flathub.trustedkeys.gpg to verifier
F: Fetching summary file for remote ‘gnome-nightly’
F: Adding GPG keyring data from gnome-nightly.trustedkeys.gpg to verifier
F: No installations directory in /etc/flatpak/installations.d. Skipping
F: Fetching summary file for remote ‘gnome-nightly’
F: Adding GPG keyring data from gnome-nightly.trustedkeys.gpg to verifier
F: Transaction: install gnome-nightly:runtime/org.gnome.Sdk/x86_64/master[*]
F: Updating remote metadata for gnome-nightly
F: marking op install:runtime/org.gnome.Sdk/x86_64/master resolved to c6f3add218ed20a8dce64068cb95bb7e0d78936b3ddd765a090ffc58e152dad7
F: Transaction: install/update gnome-nightly:runtime/org.gnome.Sdk.Locale/x86_64/master[/en]
F: Transaction: install/update gnome-nightly:runtime/org.freedesktop.Platform.GL.default/x86_64/20.08[$old]
F: Transaction: install/update gnome-nightly:runtime/org.freedesktop.Platform.openh264/x86_64/2.0[$old]
F: Transaction: install/update gnome-nightly:runtime/org.freedesktop.Platform.VAAPI.Intel/x86_64/20.08[$old]
F: marking op install/update:runtime/org.freedesktop.Platform.VAAPI.Intel/x86_64/20.08 resolved to 30ae550718814b6382b74319473e6f0acfd4b76be512f4cfa4c1832bd542d3ff
F: marking op install/update:runtime/org.freedesktop.Platform.openh264/x86_64/2.0 resolved to 4084792068caa7755e04a77367493c0adca7efb12c38572c1e198b8b0566b7f8
F: marking op install/update:runtime/org.freedesktop.Platform.GL.default/x86_64/20.08 resolved to ccc14d89764f9c6855c8e196a2b25b3a40f06409f6b0276df232f4a86c35f442
F: marking op install/update:runtime/org.gnome.Sdk.Locale/x86_64/master resolved to 3a41fe0cdaede4fd392625a397c54ee161ccc2470a1014c04b2e345b342a7ee7
1. org.gnome.Sdk x86_64 master gnome-nightly < 662.5 MB
2. org.gnome.Sdk.Locale x86_64 master gnome-nightly < 337.5 MB (partial)
3. org.freedesktop.Platform.GL.default x86_64 20.08 gnome-nightly < 42.3 MB
4. org.freedesktop.Platform.openh264 x86_64 2.0 gnome-nightly < 1.5 MB
5. org.freedesktop.Platform.VAAPI.Intel x86_64 20.08 gnome-nightly < 11.2 MB
Installing 1/5… F: Preparing transaction in repository 0x5649bfb953e0
F: Pushing lock non-blocking with timeout 30
F: Creating repo lock table
F: Opening repo lock file
F: Push lock: state=unlocked, depth=0
F: Locking repo shared
F: Using new tmpdir staging-0117d4ec-1de0-4ff7-84a5-450f9d40d1a6-JURbbf
F: Loaded gnome-nightly summary from cache
F: Adding GPG keyring data from gnome-nightly.trustedkeys.gpg to verifier
F: starting fetch of c6f3add218ed20a8dce64068cb95bb7e0d78936b3ddd765a090ffc58e152dad7.commit (detached)
F: fetch of c6f3add218ed20a8dce64068cb95bb7e0d78936b3ddd765a090ffc58e152dad7.commit (detached) complete
F: _ostree_fetcher_should_retry_request: error: unset, n_retries_remaining: 5
F: Adding GPG keyring data from gnome-nightly.trustedkeys.gpg to verifier
F: pull: idle, exiting mainloop
F: Loaded gnome-nightly summary from cache
F: Adding GPG keyring data from gnome-nightly.trustedkeys.gpg to verifier
F: starting fetch of c6f3add218ed20a8dce64068cb95bb7e0d78936b3ddd765a090ffc58e152dad7.commit (detached)
F: fetch of c6f3add218ed20a8dce64068cb95bb7e0d78936b3ddd765a090ffc58e152dad7.commit (detached) complete
F: _ostree_fetcher_should_retry_request: error: unset, n_retries_remaining: 5
F: Adding GPG keyring data from gnome-nightly.trustedkeys.gpg to verifier
Installing 1/5… ████████████████████ 100% 336 bytes/sF: pull: idle, exiting mainloop
F: Committing transaction in repository 0x5649bfb953e0
F: txn commit staging-0117d4ec-1de0-4ff7-84a5-450f9d40d1a6-JURbbf
F: Popping lock non-blocking with timeout 30
F: Pop lock: state=shared, depth=1
F: Unlocking repo
Installing 1/5… ████████████████████ 100% 168 bytes/sF: No checksum specified, getting tip of runtime/org.gnome.Sdk/x86_64/master from origin gnome-nightly
F: tip resolved to: c6f3add218ed20a8dce64068cb95bb7e0d78936b3ddd765a090ffc58e152dad7
Error: While trying to checkout c6f3add218ed20a8dce64068cb95bb7e0d78936b3ddd765a090ffc58e152dad7 into /home/ivans/.local/share/flatpak/runtime/org.gnome.Sdk/x86_64/master/.c6f3add218ed20a8dce64068cb95bb7e0d78936b3ddd765a090ffc58e152dad7-3YP1S0: Opening content object b2732cad3f3503e1be2f5e89283201d1e3aee8728ca6115dc1d87e9cbcff2592: Couldn't find file object 'b2732cad3f3503e1be2f5e89283201d1e3aee8728ca6115dc1d87e9cbcff2592'
F: Free lock: state=unlocked, depth=0
F: Closing repo lock file
F: Free lock table
error: Failed to install org.gnome.Sdk: While trying to checkout c6f3add218ed20a8dce64068cb95bb7e0d78936b3ddd765a090ffc58e152dad7 into /home/ivans/.local/share/flatpak/runtime/org.gnome.Sdk/x86_64/master/.c6f3add218ed20a8dce64068cb95bb7e0d78936b3ddd765a090ffc58e152dad7-3YP1S0: Opening content object b2732cad3f3503e1be2f5e89283201d1e3aee8728ca6115dc1d87e9cbcff2592: Couldn't find file object 'b2732cad3f3503e1be2f5e89283201d1e3aee8728ca6115dc1d87e9cbcff2592'