I appreciate you for posting another concern in our Community forum, @6009. It's my pleasure to provide the assistance you seek concerning the software update causing close company/logoff to fail to clear all active files. 

I understand how this challenge affects the operation of your business with QuickBooks Desktop (QBDt). Let's isolate your issue by verifying and rebuilding your data in QBDT. The verify tool locates the most common problems in a company file, and the rebuild tool fixes them.

Here's how to verify your company data:

1. Go to Window, then click Close All.
2. Go to File, then hit Utilities.
3. Choose Verify Data. If you see: 

• QuickBooks detected no problems with your data—your data is clean, and you don’t need to do anything else.
• An error message—search for it on our QBDT support site for how to fix it.
• Your data has lost integrity—Data damage was found in the file. Rebuild your data

Please follow the steps below to rebuild your company file data:

1. Go to File, Utilities, then click Rebuild Data.
2. Follow the on-screen instructions, then select OK. 
3. Choose where you want to save your backup, then hit OK. 
4. Type in a new name in the File name. Click Save.

For more detailed steps, you can read this article: Verify and Rebuild Data in QuickBooks Desktop.

You may want to use these articles as your resources in handling files in QuickBooks Desktop:

• Import and export data in QuickBooks Desktop
• Export lists from the old company file into a new data file

You are always welcome to post in the Community with any QuickBooks-related questions you may have. We're available 24/7. have a nice day!