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deposit_update: Drop the unneeded check on the directory_missing call

Antoine R. Dumont requested to merge generated-differential-D4059-source into generated-differential-D4059-target

We are working with a SWHID generated by the deposit which is already tested in another way. This checks is thus redundant.

Related to !377 (closed)

Test Plan

tox

Migrated from D4059 (view on Phabricator)

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