MS has a document describing 6 cases where a file cannot be deleted, with remedies. From your description, your situation is covered under the heading "Cause 5".
Cause 5: The file name includes a reserved name in the Win32 name space
If the file name includes a reserved name (for example, "lpt1")
in the Win32 name space, you may not be able to delete the file. To
resolve this issue, use a non-Win32 program to rename the file. You
can use a POSIX tool or any other tool that uses the appropriate
internal syntax to use the file.
Additionally, you may be able to use some built-in commands to bypass
the typical Win32 reserved name checks if you use a particular syntax
to specify the path of the file. For example, if you use the Del
command in Windows XP, you can delete a file named "lpt1" if you
specify the full path of the file by using the following special
syntax:
del \\?\c:\path_to_file\lpt1
For more information about
deleting files with reserved names under Windows NT and Windows 2000,
click the following article number to view the article in the
Microsoft Knowledge Base:
120716 How to remove files with reserved
names in Windows
For more information about deleting files with
reserved names under Windows XP, click the following article number to
view the article in the Microsoft Knowledge Base:
315226 How to
remove files with reserved names in Windows XP
If you open a handle
to a file by using the typical Win32 CreateFile mechanism, certain
file names are reserved for old-style DOS devices. For backward
compatibility, these file names are not permitted and they cannot be
created by using typical Win32 file calls. However, this issue is not
a limitation of NTFS.
You may be able to use a Win32 program to bypass the typical name
checks that are performed when a file is created (or deleted) by using
the same technique that you use to traverse folders that are deeper
than MAX_PATH. Additionally, some POSIX tools are not subject to these
name checks.
So I'd recommend you try:
del \\?\C:\Users\DOBRE\AppData\Local\MyApps\CygWin\usr\share\avogadro\crystals\zeolites\CON.cif