I am able to read and write sectors directly with INT 13H Extended Read
(42H) and Extended Write (43H) calls (for details see INT13EXT.VXD Thread).
Windows does not seem to mind, but the problem is that is does not know
about any changes since it has some sectors cached. Is there anyway to
inform Windows to re-read after I change sectors?

I've also tried using INT 25H and INT 26H and the reading works fine and
writing works fine to floppy only.  Writing to hard drives locks the system.

I've also tried using INT 21H AX=7305H CX=FFFF however the same thing
happens as INT25H and INT26H above.

In reading the Interrupt list at http://www.*-*-*.com/
that:
Windows98 will display an error message and deliberately hang the system on
attempted write to any hard disk if neither bit 7 of the Extended Drive Info
byte nor bit 6 of "DOS_FLAG" (List-of-Lists+60h) is set.  I would assume
this is what is happening to be.

Does anyone know how I could use these other two ways and not have the
system lock up?  Where can I get the Extended Drive Info?

Best Solution would be:

Is there a windows approach to read/writing sectors directly (so that
windows knows they have changed on writes) instead of this BIOS approach?  I
know if I had Windows NT I could just open \\.\C:.

Thanks,