You are creating an "Update Issue" Action in Jira.

You are configuring the Issue ID with a pill, like in the attached printscreen. 

You are noticing that the Additional Fields is greyed out (see same printscreen)

Note: For the case in which your Issue ID contains the static Issue ID in Jira please follow this article.

To overcome this, you will need to add an action in the flow before the Update Issue action.  This action will take name values as inputs.

1. In Flow Designer press "Create New Action"

 2. Then press "Create Input"

and

3. Add Input Variables as in the model below

4. You then press the "+" sign in the Action Outline and select from "Utilities" the "Script" option

5. Fill in the Input Variables and the Script, and Output Variables as below:

6. In the "Outputs" of the "Action Outline" you would have your Action Output defined as in the below mode:

7. You then create an action prior to "Update Issue" ( in this example called "generate_additionalfields")

8. You are now ready to  drag and drop the "Encoded query" value in the Additional fields

To test this you would create an Issue in Jira, (called DP-16 in this example)

And in ServiceNow you would populate the description of your record as the Jira record name ( in this case DP-16)

You should then see a Success Message

The script used in the current example, on Step number 5 is the following:

(function execute(inputs, outputs) {
var nameValues = JSON.parse(inputs.nameValues);
var encodedQuery = "";
var keys = Object.keys(nameValues);
for (var i = 0; i < keys.length - 1; i++) {
encodedQuery += keys[i] + "=" + nameValues[keys[i]] + "^";
}
encodedQuery += keys[i] + "=" + nameValues[keys[i]];
outputs.encoded_query = encodedQuery;
})(inputs, outputs);