I'm trying to test it right now on my Linux PC with Ubuntu 14.04, I'll let you know as soon as as it finishes installing. However I must point out that on https://software.intel.com/en-us/articles/flash-tool-lite-user-manual it says only Ubuntu* 12.04 LTS 64 bits supported. I'll get back to you as soon as possible.
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I actually had a similar issue to yours.
But I followed the steps bellow:
1. dpkg --get-selections | grep -v deinstall
To check all the installed packages.
You should be able to find a line like this:
2. sudo dpkg --force-all -r phoneflashtoollite
To force remove phoneflashtoollite
3. sudo gdebi phoneflashtoollite_126.96.36.199_linux_x86_64.deb
To install the FTL package.
4. Press the down key until OK is red highlighted and press enter.