retraction settings are wrong.

Each time the printhead moves from one print to another it retracts the filament. and feeds back to start printing.

Now, you have a bowden tube based printer, so need longish retractions.
With a flexible filament there is ALWAYS some contraction and expansion when you retract.

So you need to use very slow retractions - and weirdly counter intuitively - as short as you can get away with.

Looking at it that part should normally print all the way through without needing to use retractions.
So the single part prints fine.

It's only when you start using retractions between models for each layer, you get problems.

Sooo, SLOW your printspeed right down (slower than you were just thinking :-)
say somewhere between 10-20 mm/s.
Reduce the travel speed of the printhead - say 50mm/s to start - slower if necessary. This gives more time for both the retraction and re-extrusion to work properly.
And reduce the speed of your retractions to around 30-40mm's. Less if it's already at that.
Retraction length wise. basically as short as t#you can get away with. start at maybe 3mm and work your backwards till you start to get stringing - at which point it's too short.

You do have an advantage in that you are using 3mm filament - which reduces the compression of the filament. But obviously not sufficiently :-)

Getting multiple prints with flexible filament is something of an artform - so good luck :-)