I would be surprised if you did actually manage to delete your XBMC XBE. My money's on your old copy just being really, really old. After all, if the file couldn't be found, you'd likely get a BIOS error.
It's possible to flash the TSOP (the chip on the X-Box motherboard that holds the retail BIOS). This process provides nearly all the perks of a modchip... Without the actual modchip. Can't be done with a 1.6 X-Box, though.
This particular boot sequence sounds like the X2 5035. Quite a nice BIOS, that one, even if it's too big to fit into most TSOPs. Uses a config file on the HDD for it's settings so you don't have to reflash every time you wanna change something. Probably worth taking a look at that file when you fix this to prevent further issues (setup a secondary dashboard for example, and make sure DVD booting is correctly enabled. It's called "x2config.ini" and it should be sitting on the root of E:).
That is to say, there's the X2 chips, and then there's the X2 BIOSes. Kinda like how there's EvoX BIOSes and an EvoX dashboard.
It's possible to switch BIOS banks in the earlier console revisions, but even if you went to the trouble you'd likely only end up restoring the stock version. That's not much good to you.
Anyway!
Xplorer360 lets Windows read/write to X-Box drives. Keep in mind you'll have to hotswap if yours is locked (which is likely if you're still using the stock HDD).