Updating multivalue fields can be a bit tricky when you want to change a specific value in the collection. You could try the following:

1. Create a new empty multivalue token in your workflow (something like NewValues)
2. Retrieve the multivalue field (set it to All Values)
3. Iterate the values using a for each value (under Values select the YourToken_All value from the retrieve field values activity)
4. Add a two-branch condition
   1. If ForEach_Iteration = Your target value
      • Append the new value to %(NewValues)
   2. Else,
      • Append the %(ForEach_CurrentValue)
5. Add a Set Field Values, and Replace the current values with the %(NewValues) token

What this does is build a new list of values, in the same order, that only replaces the target value. Then, that new list overwrites the old list allowing you to change a specific value.

You may need to account for the unexpected, for example, if the process is trying to update the 4th value but there are only 3 current values.