What I ended up doing is to use Selenium to script opening each issue and assigning an organization. I used JQL (issue search) to list all of the tickets, copied the issue ID's, made that an array in a selenium script, and ran it on the array. The script was not very good, I'm sure if I had more than a hundred I would have worked harder to make it better, but this worked well enough, took a while to do them one at a time but it was just a hack,
Replace MyCompany (part of your Atlassian url), MyOrganization (name of the organization you want to set), and MyDeskID (the issue prefix for service desk) and of course the array of issue ID's...
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head profile="http://selenium-ide.openqa.org/profiles/test-case">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<link rel="selenium.base" href="https://mycompany.atlassian.net/" />
<title>New Test</title>
</head>
<body>
<table cellpadding="1" cellspacing="1" border="1">
<thead>
<tr><td rowspan="1" colspan="3">New Test</td></tr>
</thead><tbody>
<tr>
<td>storeEval</td>
<td>myArray = new Array('52', '51', '50', '48', '47', '46', '45', '44', '43', '42', '41', '40', '39', '38', '37', '36', '35', '34', '33', '32', '31', '30', '29', '28', '27', '26', '25', '24', '23', '22', '21', '20', '19', '18', '17', '16', '15', '14', '13', '12', '11', '10', '9', '4');</td>
<td>myArray</td>
</tr>
<tr>
<td>storeEval</td>
<td>0</td>
<td>index</td>
</tr>
<tr>
<td>while</td>
<td>index < storedVars['myArray'].length;</td>
<td></td>
</tr>
<tr>
<td>store</td>
<td>javascript{storedVars['myArray'][storedVars['index']]}</td>
<td>issueid</td>
</tr>
<tr>
<td>echo</td>
<td>javascript{storedVars['issueid']}</td>
<td></td>
</tr>
<tr>
<td>storeEval</td>
<td>"https://mycompany.atlassian.net/browse/MYDESKID-"+storedVars['issueid']</td>
<td>myURL</td>
</tr>
<tr>
<td>echo</td>
<td>javascript{storedVars['myURL']}</td>
<td></td>
</tr>
<tr>
<td>open</td>
<td>javascript{storedVars['myURL']}</td>
<td></td>
</tr>
<tr>
<td>click</td>
<td>css=span.trigger-label</td>
<td></td>
</tr>
<tr>
<td>waitForPageToLoad</td>
<td></td>
<td></td>
</tr>
<tr>
<td>pause</td>
<td>2000</td>
<td></td>
</tr>
<tr>
<td>click</td>
<td>id=customfield_13300-textarea</td>
<td></td>
</tr>
<tr>
<td>sendKeys</td>
<td>id=customfield_13300-textarea</td>
<td>MyOrganization</td>
</tr>
<tr>
<td>pause</td>
<td>1000</td>
<td></td>
</tr>
<tr>
<td>click</td>
<td>link=MyOrganization</td>
<td></td>
</tr>
<tr>
<td>click</td>
<td>id=edit-issue-submit</td>
<td></td>
</tr>
<tr>
<td>echo</td>
<td>javascript{storedVars['index']}</td>
<td></td>
</tr>
<tr>
<td>storeEval</td>
<td>storedVars['index'] + 1;</td>
<td>index</td>
</tr>
<tr>
<td>echo</td>
<td>javascript{storedVars['index']}</td>
<td></td>
</tr>
<tr>
<td>pause</td>
<td>2000</td>
<td></td>
</tr>
<tr>
<td>endWhile</td>
<td></td>
<td></td>
</tr>
</tbody></table>
</body>
</html>
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