Hi graydenh,
Yes, the UpdateProjectProperty workflow activity allows you to update a multi-value custom field.
For a multi-value project custom field, the UpdateProjectProperty activity will add the value to the selected values, so previously selected values are not deselected.
You can also only add one value at a time using the UpdateProjectProperty activity. So if you need to specify multiple values, you need to have multiple UpdateProjectProperty activities in your workflow.
I hope this helps,
Hans
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