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Hi, Thanks for the reply.
When the tool change script pull the filament back, it creates a tiny string, when the other filament is loaded that string is "pushed" foward, but not all of it, after some tool changes these strings make a small ball, and block the passage on the middle of the E3DV6 hotend, in the part where the pfte tube meets the heatbreak (which also has an internal pfte tube for better heat blockage),

i'm only using 2 filaments right now, i didnt received the relay board yet, and the material is ABS+ from a local supplier, its a very good filament, but i'll try using another just to make sure.

My tool change is the following

STARTING SCRIPT
M140 S[bed0_temperature] ; set bed temp, no wait
M104 S[extruder0_temperature] ; set extruder temp, no wait
G21 ;metric values
G90 ;absolute positioning
M107 ;start with the fan off
;M150 R255 U255 B255 P4 ;Change LED Color to white

G28
G29

T1 ;first prime T1 and move it back
G92 E0
G1 Y0 F5000
G1 X10 E50 F500
G92 E0
G1 F3000 E-350
G92 E0
T0 ;then prime T0
G92 E0
G1 F3000 E350
G92 E0
G1 Y1
G1 X160 E50 F500
G92 E0
G1 F{travel_speed}
;Put printing message on LCD screen
M117 3DNinja Printing...

TOOL CHANGE SCRIPT
G91
G1 Z2

T[old_tool]
G1 E-10 F6000 ; retract the filament from melting zone
G4 P2000
G1 E5 F3000
G4 P3000
G1 E-345 F3000

T[new_tool]
G1 E340 F3000
G1 E10 F2000
G1 Z-2

G90

I have tried to make the filament go inside again and wait a bit, it helped, but didnt fixed the issue. I'm trying now to cool the nozzle before changing the filament, but thats gonna cost arount 30s for every switch, for some parts this may be a lot.