Since there are no checkpoints (yet) for a running task, the task has to start from scratch after a BOINC client restart due to whatever reason.
However such a restart always ends into an error.

Part of the result of the initially start of a task:

09:20:23 (4300): wrapper (7.7.26016): starting
09:20:23 (4300): wrapper: running get_fraction_done.bat (ligands.sdf docking_log fraction_done.txt 500 TARGET_PRO_1.mol2)
09:20:23 (4300): wrapper: running worker.bat ( 500 TARGET_PRO_1.mol2)
        1 file(s) moved.
ECHO is off.

Part of the result after a restart of a task:

11:47:45 (3140): wrapper (7.7.26016): starting
11:47:45 (3140): wrapper: running get_fraction_done.bat (ligands.sdf docking_log fraction_done.txt 500 TARGET_PRO_1.mol2)
11:47:46 (3140): wrapper: running worker.bat ( 500 TARGET_PRO_1.mol2)
        1 file(s) moved.
The requested operation cannot be performed on a file with a user-mapped section open.
11:47:52 (3140): worker.bat exited; CPU time 0.000000
11:47:52 (3140): app exit status: 0x1
11:47:52 (3140): called boinc_finish(195)

Hello Crystal Pellet!

Explain please - this error occurs after restart of BOINC only, not computer?

Hello Crystal Pellet!

Explain please - this error occurs after restart of BOINC only, not computer?

At every restart of the task, the task starts from the very beginning, because no checkpoints of the job are written. As stated before that tasks errors out.

A task will restart when BOINC-client restarts (thus also after a boot).

When you suspend a task, the task will stay in memory and will run further from that point after a resume even without a checkpoint.
A feature of BOINC is to keep a task in memory until the first checkpoint, even when you had set to not keep a suspended task in memory, cause it will never achieve the first checkpoint.

The requested operation cannot be performed on a file with a user-mapped section open.

This error can be a result of antivirus check after a file was released by software.
So when software tries to delete or move a file that is in checking state by antivirus it can fail with this error.
User can try to turn off antivirus.
Or software developer can sign exe with certificate so that antivirus could trust it.

The error after BOINC's restart can be avoided.
The problem is the MOVE-command. It tries to move a non-existing file.
I solved this by replacing in rbdock-boinc_11.4_windows_x86_64.bat (in slot renamed in worker.bat) the line

MOVE target.mol2 %targetmol2%

with following lines

IF NOT EXIST target.mol2 GOTO alreadymoved
MOVE target.mol2 %targetmol2%

:alreadymoved

Crystal Pellet, thank you for notice!

Crystal Pellet, thank you for notice!

My pleasure!

It could be done simpler by replacing the line

MOVE target.mol2 %targetmol2%

by one line

IF NOT EXIST %targetmol2% MOVE target.mol2 %targetmol2% >NUL

Here we changed input files a little bit, so it is not needed to rename the file.