Sounds like it should be possible.
Of course you will need to make sure that chkdsk is available in the preboot environment you plan to boot from PXE into.
I presume that you plan to use WinPE, but I'm not sure if Microsoft provides chkdsk as part of WinPE or not. Create a job that runs a script that runs chkdsk and see what happens.
If chkdsk is not part of WinPE, then you need to find chkdsk and add it to your boot image yourself. Will chkdsk run in WinPE??? Remember that WinPE does not support running any old DOS applications like Windows does. All the DOS support parts of Windows are not part of WinPE, so you'll need a chkdsk that is not DOS based that will run in WinPE.