The most common reason a full backup fails is the voicemail is busy, or thinks it is busy (a port locked up, file is "open", or something), but I don't know of a way to restart just the VM service like on a 3300...
I would perform the highest level backup you can, in case of corruption of the SD card at least you have something, and hopefully you have a text/paper copy of the database. Remember that if they reboot and the system CF is corrupt, there is potential the system will not boot and the data won't be recoverable...
As far as the CF goes, the only thing I have had luck doing is duping a new Mitel flash card to a off the shelf one with Linux using dd... Otherwise something happens when you first boot a CF in a CX, MX or AX that kind of messes it up if you try to move it to another platform, at least in my experience. Remember that the CF cards from Mitel, although not "special", are designed for very high write cycles, much higher than average consumer grade CF cards.
FWIW, you can still get official CF cards from Mitel and their resellers... I just got one in a couple days ago ordered from Jenne.
I also don't use kermit anymore... can't remember the last time I did a kermit backup or restore, maybe 5+ years ago or so... I do everything via IP if at all possible. I have had a ton of problems with the new Filezilla server though, and switched to Core FTP LE server a few months ago.