This actually appears to be caused by ABS. Moderator(s), if any, please move this as applicable.
I continued to investigate, swapped the script for a batch file to run locally on the remote system via TestComplete instead, reduced the # of steps performed, etc. and found that this loss of permissions occurs when ABS shuts down the TestComplete script.
ABS -
1. Run Submacro 'StartVM' using PowerCLI script
2. Starts and runs TestComplete macro on the VM
3. Stops TestComplete/TestExecute on the VM after last macro step
4. Run Submacro 'StopVM' using PowerCLI script
5. Stops ABS macro
By continually attempting to access the folder I found that it locks at Step 3. I disabled Step 4 to rule out the PowerCLI script. The padlock appears on the folder icon as the TestComplete 10 Log appears on the VM, indicating that the TestComplete test has, well, completed, and before ABS completes the run.
Edit: Attached screenshot of the error displayed when I attempt to take ownership and restore permission accounts.
