Flashing Folder Icon Sometimes

ChesterWilkinson wrote:

I am running two third party SSD's

It is a 15" Pre-retina Mid 2012 MacBook Pro running macOS Mojave. I was wondering if it is anything to do with the boot drive being formatted as APFS (Encrypted) however I do not remember formatting the drive as this (I thought I just did it as APFS standard).

Verify your startup disk is in the main HDD bay, not the secondary DVD caddy bay.

disable FileVault form the >system Preferences>FileVault this could take some time to complete.

You can always reformat again the parent drive as apfs non encrypted , reinstall the macOS, and from a backup restore your user data in an effort to resolve the issue.

Try re-selecting the Macintosh HD in the Startup Disk Manager

>System Preferences>Startup Disk

unlock the padlock and highlight the Macintosh HD

How to select a different startup disk - Apple Support

further info:

About the screens your Mac displays as it starts up - Apple Support

If your issue continues Boot into Recovery (Command R) and from the dropdown menu: Utilities>  Disk Utility> run the First Aid on your Macintosh HD. If errors are found and repaired, run again until no errors reported.


Recovery http://support.apple.com/kb/HT4718

ChesterWilkinson wrote:

Sorry, I forgot to mention that I have already tried this too, I have also tried to repair the disk and no errors were found.

You do not say what exact Mac /model /year /size /retina /touchbar is this ?

or what exact macOS ?

From Recovery you can reinstall the macOS on top of your existing macOS for a renewed copy—this leaves all user files/data in place. Recovery  http://support.apple.com/kb/HT4718

Always advised to have a current back up plan.