It seems the .vmxf filetype, which was first introduced in VMware Workstation, is now used on ESXi as well.
It looks as if that .vmxf file is created when VMware Tools are installed on specific Guest OS.
But the information is scarce, or well hidden.
In Virtual Machine Files it just states "Additional virtual machine configuration files"
Judging by the content of these .vmxf files, it looks as if they only contain VMware Tools information.
Interesting is this Packer Issue#7140.
It seems their cleanup procedure had an issue with the .vmxf file as well.
The remark from the issue submitter
- The .vmxf file only appears after VMWare Tools has been installed in Windows and the Windows VM has been rebooted.
seems to confirm the file is VMware Tools related.
And I indeed only see the file on my VMs that run a Windows Guest OS.
But that doesn't solve your original issue.
As another poster previously stated, you could remove that file.
But instead of using a SSH session, use the PowerCLI Datastore provider and the Remove-Item cmdlet.