I also have a 2013 2.2d Portfolio, around 3 four months ago the Eco Stop/Start stopped working. No other symptoms, everything else was fine. I only had an old Battery Charger which is no use for AGM Batteries so got myself a Ctex MSX5 Charger. I connected it to the small Battery first (Positive to battery port, negative to a bolt on the chassis) and it charged the Battery reasonably quickly. I then similarly connected it to the main Battery after a few seconds, the fault light started to flash on the Charger. I double-checked I had connected it correctly and retried with the same result. The instructions for the Charger advised that if this was the case the Battery was either 1) Heavily Sulphated, 2) Cannot be charged or 3) Cannot hold a charge and in all three instances would require replacement. The car was still starting effortlessly but bearing in mind it was six years old (Original) and that we were coming up to Winter I sourced an Exide Replacement online from Tayna Batteries for £136 delivered next day. After fitting the Battery and resetting the BMS and the Electric Windows, this cured the Eco Stop/Start Fault. I would suggest that if your car still has the original Battery fitted it will be at or near the end of its productive life.
The Ctex is a godsend now that we are in Lockdown as the car is very rarely used. I have fitted the Ctex Comfort Fit & Battery Indicator, so I can check when I need to top up the charge as I have installed the indicator in a small opening cut in the boot sidelining (Template supplied). Using those mentioned above, it is merely a case of connecting the Charger to the inlet plug inside the boot. No fiddling with clamps or even raising the boot floor