Since mbrscan/mbralign don't work on ESXi, what alternatives are available? The first thought that popped into my head was to copy the -flat.vmdk to another linux host, align it and copy it back but that will be extremely time consuming. Are there any other in-place tools that operate similarly to the way mbralign does within ESX? Thanks.
Without an ESX service console for this you need to run on Linux like you mentioned... If NFS, then you don't have to copy to Linux first, but it sounds like you are using VMFS since you are copying the file. Paragon is also an interesting tool and works inside the windows VM itself to realign within the LUN (needs some free space). One of our astute customers told us about it and we tested internally and in our own I.T. group and it worked as advertised. If a C: drive it reboots and other drives go offline but the vm stays up and it aligns without copying to a new vmdk. It does need some free space in the vmdk though.
If an nfs datastore that will work... might want root access too for the linux host. make sure you have enough room for a full copy of the -flat.vmdk file and also to clean up -mbralign-backup files after you confirm all is working ok.