Maybe you didnt add enough sodium carb to begin with. Maybe you filtered too quick before solids appeared?
In any case, your alkaloids are probably in the solids there, together with excess sodium carbonate.. Just put that, together with the stuff that precipitated before, and redissolve in acidic solution. Notice a lot of the acid will be just to neutralize the sodium carbonate, so if you add vinegar, it will start foaming, and keep foaming as you add and mix, untill all the sodium carb is neutralized and then the pH starts being acidic. Once you have it in acidic solution, filter and saturate with salt
If you alternate salt precipitation with base precipitation, whenever you redissolve the salt, you just need some hot water, no need for acid, so this is good because when you precipitate with base, you dont waste a lot of base to neutralize the acid..
And yeah dont throw anything away until youre finished.