I was experiencing similar delamination of shell layers in some stuff I was printing in PETG - especially when thinner sections were subject to bending or twisting stresses. I'd had better luck in cases where I could have thinner parts printed directly on the heated bed (I've read that material bond strength generally increases with temperature), but this usually isn't an option. Drove me nuts! I'll describe what helped me with the hope that it conveys something useful. The basic idea is to get the side surfaces of those shell layers right up against each other to promote good thermal bonding - in part by tweaking the Extrusion Multiplier and Extrusion Width parameters.
BACKGROUND: S3D uses three parameters to estimate the extrusion speed required to achieve your specified layer width per length traveled. These are Filament Diameter, Nozzle Diameter (fixed), and Extrusion Multiplier. I measured and entered my filament diameter. I then printed a 20x20x2 mm cube with one shell layer and no top or bottom layers and then measured/averaged the four wall thicknesses (i.e. Extrusion Width). This along with the current settings in S3D for Extrusion Width and Extrusion Multiplier gave me the information I needed to calibrate the Extrusion Multiplier parameter.
Extrusion Multiplier (calibrated) = Extrusion Multiplier (setting) x [Extrusion Width (setting)/Extrusion Width (measured)]. This calibration estimated the speed with which S3D should tell my printer to extrude filament - per mm traveled - to achieve the specified Extrusion Width at the specified Layer Height.
BACKGROUND (Cont'd): Based upon what I've read, S3D uses only one parameter, Extrusion Width, to calculate the horizontal distance between the center lines of adjacent layers. So... the extrusion rate AND the horizontal layer spacing BOTH have to be set correctly (compatibly?) to optimize bond strength. In other words, the layer width, and the distance between layer centers must be set to promote inter-layer contact.
After entering the measured Extrusion Width and the calibrated Extrusion Multiplier into S3D (Extruder tab), I prepared to print. Zooming close in from a top view in Preview Mode I could see that there were small gaps between my perimeter shell layers... especially where I was observing delamination on previous prints! I went back and forth between editing my process and checking Preview Mode - increasing S3D's Extrusion Width setting - until the spaces between shell layers had disappeared.
I printed another trial, and found that while the shell layer bonds had improved, they still delaminated when flexed significantly.
I increased my Extrusion Multiplier from 0.91 (calibrated) to 0.95, and the resulting print exhibited no further delamination when flexed.