Here the help message Phabricator returns about message deletion:
Be careful when deleting users! This will permanently and irreversibly destroy this user account.
If this user interacted with anything, it is generally better to disable them, not delete them. If you delete them, it will no longer be possible to (for example) search for objects they created, and you will lose other information about their history. Disabling them instead will prevent them from logging in, but will not destroy any of their data.
It is generally safe to delete newly created users (and test users and so on), but less safe to delete established users. If possible, disable them instead.
Phabricator accounts are independant, and can be linked and unlinked with other identity providers (here Wikimedia LDAP and WP OAuth).
Did you create two accounts on Phabricator? If so, you can with the first account go to your preferences (the tool icon at the right), choose External accounts and delete your MediaWiki user, then readd it on this account.
Do you experience some other problem? If so, explain what you try to achieve and what error do you get.