Launched in early June, the plug-in provided a way to run Microsoft Outlook on Google Apps instead of Microsoft Exchange. Sadly for Google, the plug-in didn’t play well with Outlook, most notably making its data inaccessible to Windows Desktop Search. Now, after a few weeks of troubleshooting and some help from Microsoft (that must have made for some interesting conference calls), the company has found a solution to the problem and a fix has been released.

“We worked closely with Microsoft to address two issues that we shared recently, and we appreciate their help,” Google Apps Senior Product Manager Chris Vander Mey said in a company blog post Tuesday. “The Windows Desktop Search feature now works, so you can choose between the native Outlook search, which has been available since launch, and Windows Desktop Search to find information in Outlook.”

With that little snafu resolved, it’s now back to business for Microsoft (MSFT) and Google (GOOG), with the former attacking the latter’s search business and the latter steadily encroaching on the former’s software turf. We now return you to our previously scheduled hostilities…

“The installation of the Google Apps Sync plugin disables Outlook’s ability to search any and all of your Outlook data,” Microsoft explained in a post to the Outlook Team blog. “When a Google Apps user installs the sync plugin for Outlook, the plugin modifies a registry key which disables Windows Desktop Search from indexing and providing search functionality for all Outlook data, not just the Outlook data being synchronized from GMail. Because Outlook search relies upon the indexing performed by Windows Desktop Search, Outlook search functions are broken as a result. It is also important to note that uninstalling the plugin may not fix the issue.”

Uh-oh. Good luck finding that budget-request email you sent to your CFO a few months ago….

Google (GOOG) is working with Microsoft (MSFT) to resolve the issue, but the damage may have already been done. Enterprise is notoriously reluctant to embrace change specifically because of cock-ups like this. Enterprise likes familiarity. It likes seamless change. With Apps Sync for Outlook, Google provided the former, but it fell short on the latter. And that may inspire some companies that had been considering Apps Sync for Outlook to stick with Exchange for a while longer.

“The installation of the Google Apps Sync plugin disables Outlook’s ability to search any and all of your Outlook data,” Microsoft explained in a post to the Outlook Team blog. “When a Google Apps user installs the sync plugin for Outlook, the plugin modifies a registry key which disables Windows Desktop Search from indexing and providing search functionality for all Outlook data, not just the Outlook data being synchronized from GMail. Because Outlook search relies upon the indexing performed by Windows Desktop Search, Outlook search functions are broken as a result. It is also important to note that uninstalling the plugin may not fix the issue.”

Uh-oh. Good luck finding that budget-request email you sent to your CFO a few months ago….

Google (GOOG) is working with Microsoft (MSFT) to resolve the issue, but the damage may have already been done. Enterprise is notoriously reluctant to embrace change specifically because of cock-ups like this. Enterprise likes familiarity. It likes seamless change. With Apps Sync for Outlook, Google provided the former, but it fell short on the latter. And that may inspire some companies that had been considering Apps Sync for Outlook to stick with Exchange for a while longer.