Try not to wipe cache and user data when flashing through Flashtool.
If you can't boot to system without wiping userdata, the best way is backup via Titanium Backup before unlocking bootloader.
If I'm not wrong, Internal SD wouldn't get wiped, only /data partition. But it's better to take backup of your Internal SD first.

My Devices

Naite J105i: R1GA026 Orange [Patched Firmware] | CID: Brown
Xperia X8 E15i: MiniCM7 2.2.2 | nAa jb 06 Kernel
Xperia Mini Pro SK17i: CM 10.1 LegacyXperia | nAa 3.4 Kernel | Stolen
Xperia Neo V MT11i: Cyanogenmod 11 Nightly LegacyXperia | nAa 3.4 Kernel
Xperia L C2105: CyanogenMod 11 Nightly FreeXperia | Varun build

*Sorry for my bad english