No Z hop in Dual extruder, print getting disturbed at retraction point
It appears as though you are using (or used) an old version of Cura. More recent releases allow you to insert G-code commands on changing the extruder. You could insert a Z-hop in these sections. 

Extruder End G-code: First set the extruder in a relative mode, move up 2 mm, set absolute again:

G91
G1 Z2
G90


Extruder Start G-code: First set the extruder in a relative mode, move down 2 mm, set absolute again:

G91
G1 Z-2
G90


You could even do filament retractions to prevent oozing or stringing!

Note that this assumes both hotends are on the same carriage!



An alternative you could try is to use a print server that is able to inject G-code scripts, an example is OctoPrint: