Yeah I fixed it by editing the patch versions while making the ciaNormaly when installing stuff from eshop, it makes entries inside import.db/title.db located on your sd card, same as putting the icon on 3ds desktop.
Had to find the original version number from eshop patch, in my case 3.5.0 and then I applied that to the cia
The 3DS seems to recognise it now and won't bug me anymore about notifications