When already proficient with Arcana and then multi-classing into Cleric and choosing Arcana Domain it should allow you to choose a different skill, as you already have Arcana.
From the PHB section on backgrounds:
If a character would gain the same proficiency from two different sources, he or she can choose a different proficiency of the same kind (skill or tool) instead.
This rule does not say only during character creation or only when choosing a background, so it should apply in all cases.
When already proficient with Arcana and then multi-classing into Cleric and choosing Arcana Domain it should allow you to choose a different skill, as you already have Arcana.
From the PHB section on backgrounds:
This rule does not say only during character creation or only when choosing a background, so it should apply in all cases.
So just edit your sheet and get a new prof.
Problem solved.
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