After updating to the last nightly and opening Google Translate from top sites bar, this bug occurred. Instead of my sites, there were only pinned ones. In addition, the GitHub icon has disappeared (perhaps the disappearance of the GitHub icon is due to its updating?).

List of my top sites and correct displaying of GitHub icon.
N/A
Brave: 1.9.1 Chromium: 81.0.4044.83聽(Official build)聽unknown聽(64-bit)
Version: 5718ca617723806b9aacfb41108a0d911d1bde74-refs/branch-heads/4044@{#853}
OS: Linux
Hi @congard, did you take any action before this bug happened like pinned/excluded/re-ordered top sites?
Also if you don't mind, could you send me (either in this thread or Twitter DM if you prefer, same username @cezaraugusto) your NTP localStorage file? Here's the steps:
context menu -> inspect).JSON.parse(localStorage.getItem('new-tab-data')).pinnedTopSitesJSON.parse(localStorage.getItem('new-tab-data')).ignoredTopSitesJSON.parse(localStorage.getItem('grid-sites-data-v1')).gridSitesJSON.parse(localStorage.getItem('grid-sites-data-v1')).topSitesPlease note that we do not store this information and it's only available in your computer (specifically your new tab). I'm requesting it because your top sites data appear to be corrupted after the update and I need a broken profile to try to reproduce your issue. Thanks for reporting!
Hi @cezaraugusto, I didn't do anything before this happened. Just updated the browser.
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Thanks @congard, with the data you shared I was able to reproduce and just opened a pull-request.
Verification PASSED on macOS 10.15.4 x64 Catalina using the following build:
Brave | 1.8.86 Chromium: 81.0.4044.129聽(Official Build)聽(64-bit)
-- | --
Revision | 3d71af9f5704a40b85806f4d08925db24605ba25-refs/branch-heads/4044@{#979}
OS | macOS Version 10.15.4 (Build 19E287)
Went through the cases outlined under https://github.com/brave/brave-core/pull/5173#issue-400312677 and https://github.com/brave/brave-core/pull/5173#issuecomment-617724800 x2 times to ensure everything was working as expected.
Populated several tiles on the NTP using 1.7.98 CR: 81.0.4044.113 as per the following:

Updated to 1.8.86 CR: 81.0.4044.129 and ensured that I didn't lose any tiles on the NTP:

Used the script from https://github.com/brave/brave-core/pull/5173#issue-400312677 and ensured that both https://translate.google.com and https://github.com/congard where added in the correct positions:

Verification passed on
Brave | 1.8.86 Chromium: 81.0.4044.129聽(Official Build)聽(64-bit)
-- | --
Revision | 3d71af9f5704a40b85806f4d08925db24605ba25-refs/branch-heads/4044@{#979}
OS | Windows聽10 OS Version 1803 (Build 17134.1006)
Went through the cases outlined under https://github.com/brave/brave-core/pull/5173#issue-400312677 and https://github.com/brave/brave-core/pull/5173#issuecomment-617724800 and ensure everything was working as expected.
Populated several tiles on the NTP using 1.7.98 CR: 81.0.4044.113 as per the following:

Updated to 1.8.86 CR: 81.0.4044.129 and ensured that I didn't lose any tiles on the NTP:

Used the script from https://github.com/brave/brave-core/pull/5173#issue-400312677 and ensured that both https://translate.google.com and https://github.com/congard where added in the correct positions:

Verification passed on
Brave | 1.8.86 Chromium: 81.0.4044.129聽(Official Build)聽(64-bit)
-- | --
Revision | 3d71af9f5704a40b85806f4d08925db24605ba25-refs/branch-heads/4044@{#979}
OS | Ubuntu 18.04 LTS
Upgraded from 1.7.98. Verified no duplicate top sites.
Before upgrade:

After upgrade

Verified test plan from https://github.com/brave/brave-core/pull/5173
Used the script to generate duplicate top sites.

Most helpful comment
Thanks @congard, with the data you shared I was able to reproduce and just opened a pull-request.