Logos is "Preparing" Forever

Problem:

After an update, Logos says it is "Preparing your Library" but never finishes. The Logos Indexer shows "Stage 1 of 3".

Stage 1 of the Preparing phase, is the stage in which Logos tries to locate any new files which have been added to your Library. Depending on the size of your Library, and how many files it needs to discover, this can take a few hours. If you have already waited several hours and it hasn't moved from Stage 1, this could indicate a problem in your Windows File Structure that is preventing Logos from finding the new files, specifically because those files have been "hidden".

Tip: Reboot
Sometimes this behavior can appear if the Microsoft "Background Intelligent Transfer Service" (BITS) has been temporarily disabled by a Microsoft Update or is otherwise unresponsive. To resolve this possibility, you may wish to reboot your computer before proceeding.

Solution 1: 

It is possible malware has hidden many user directory files including Logos'.

Step 1:

End All Logos processes and open the Logos directory

1. Quit Logos.
2. Right-click Start menu
3. Click Task Manager.
4. Click the Details tab.¹
5. Click the End Process button in the bottom-right corner and close Task Manager (You may receive a warning, Click OK).
6. Right-click your Logos Icon and choose "Open file location".

The Logos directory will open but may appear empty indicating the files have been hidden. If you see "faded" folders, skip to Step 3.

¹You may need to click More details if the Details tab is not visible.

Step 2:

Show Hidden Files

Windows 10

1. At the top of the window, click the View tab and select "Options" to open the Folder Options window.
2. Click the View tab and select "Show hidden files, folders, and drives".
3. Click OK.

Step 3:

Un-hide the Logos Directory

1. At the top of the window, there will be an address, showing the location of the folder you're viewing.
2. Click the Local folder.
3. Right-Click the Logos¹ folder and select Properties.
4. Un-Check the box next to "Hidden" and click OK.
5. If you are prompted to apply changes to all sub-folders and files, do so.
6. Open Logos. It should now be able to find its files and finish Preparing your Library.

¹ The precise folder name here may differ (there may or may not be a number), but anything with Logos should be correct.

Solution 2:

BITS Troubleshooting

Logos uses BITS to download the necessary installation files. It may be possible the BITS service has been damaged, full or disabled while Logos is attempting to download installation files.
You can check this with the BITSAdmin Utility:

Using BITS Admin

Use the following command to verify whether there is a problem with BITS that is preventing Logos from downloading an update.

• Right-click Start menu
• Click Command Prompt (Admin)
• Type: "BITSADMIN /LIST" and press the Enter key.

Result 1: List of Jobs

If you receive a list of "jobs", we know BITS is enabled. If that list contains more than 50 items, it's possible that it is too full to take on moer jobs. We can clear the list to resolve this.
In most cases, "clogged" downloads are stuck in a "suspended" or "error" state and will not download on their own anyway. Use the command "BITSADMIN /RESET" to clear the list. Whatever downloads were previously listed should be cancelled and may need to be re-downloaded via their associated program at a later time.

It is recommended to run Windows Update after doing this.

Result 2: BITS does not respond

If BITS does not provide a number (not even the number 0), it may have been damaged by a virus or malware attack or disabled by your administrator so that Windows Updates can be managed at the admin level. You will need to contact your network administrator, computer manufacturer, or Microsoft for assistance in repairing or enabling BITS before you will be able to use the Logos software.