I have had a Synapse inverter for the last 5 years being used off grid.

In May last year, the batteries were replaced because the old gel batteries were no longer charging correctly.

With the old batteries connected, the system would normally shut down during the night because of low voltage and then start up again in the morning as soon as the sun hit the panels.

Since the new batteries (Hoselect 200Ah) were installed, if the system shuts down due to low voltage, it battles to start again. The 3 LEDs flash on and off continuously for hours before eventually starting. I spoke to a technician a few months ago who said it may have something to do with the cold start voltage. I've gone to the point of charging the batteries separately with a car charger and generator, and it makes no difference if they're fully charged.

Has anyone here experienced something similar? I can't seem to add a video, which would explain it more clearly

Have you perhaps measured the battery voltage after charging with a normal charger. It sounds as if those batteries are low in voltage. 

Have the batteries checked as that is the item that changed.