I did not have this happen on a site I upgraded from XF1+4.0.16 to XF2+4.1.0 Beta 2 last week. It looks like all the BB-Codes are still there. Please double-check the database that there are no xf_bb_code entries with addon_id = 'vw/vwcustom'. Possibly the BB-Codes are there but not appearing in the admin page for some reason.
What was the process used? What version was the XF1 installation on before upgrading? Did the 4.1.0 Beta 2 upgrade finish without issue, or does the add-on manager still give an Upgrade option?
If the BB-Codes are truly gone, this occurs because XenForo's add-on setup process automatically deletes all BB-Codes whenever an add-on gets upgraded due to the way XenForo has designed it. XenForo does not provide a method to disable this, so we workaround the issue by saving VaultWiki's BB-Codes to a different add-on ID. If the BB-Code step in our upgrade process was skipped for some reason, it is also possible that the add-on ID was not changed, so XenForo was able to delete the BB-Codes. This might be shown in internal-data://vw_logs/upgrade, which is a log of all the upgrade steps that were performed prior to letting XenForo perform its stock steps. The BB-Code step is generally the last or second-to-last step in the log.