What does the prefix of the raw transaction encoding of an exported Electrum transaction file (.txn) mean?
It stands for:

45505446 - EPTF - Electrum Partial Transaction Format
ff - Separator
00 - EPTF Version - This is currently always 0.

You can verify this quickly by running a python interpreter.

Python 3.6.7 (default, Oct 22 2018, 11:32:17)
[GCC 8.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
&gt;&gt;&gt; b'EPTF\xff'.hex()
'45505446ff'