I was beginning the process of extracting Syrian rue and while boiling the seeds, I was careless and went to take a dump. When I came back my kitchen was full of smoke and apparently I had underestimated how much water I needed for the first boil because it all boiled out and half the seeds are black. Did I just burn all the harmalas and ruin the extraction? It may be a dumb question, but I was really looking forward to some changa this weekend..

I would start over with fresh seeds and use more water next time. Dry seeds will absorb up to twice their weight in water when first boiled.

One time I burned a filter cake of nicely purified harmala HCl extract when the thermostat in my oven malfunctioned. When I tried to salvage the material by redissolving and resalting it, I noticed at first that there had appeared a lot of insoluble gunk and then later after filtering and salting that it would not become bright yellow as it had been before.

I discarded the material, since I do not know the purity of the remaining harmalas and, more importantly, the nature of the contaminants introduced by the charring.

If at first you don't succeed...

But yeah, I agree with pitubo in the sense that it would likely be best to start over. How big is your extraction? 100g? 300g? 1000g?

I'm only asking because it may be wise to use two pots next time, or one bigger pot (like those big chili pots) and use plenty of water. Enough to cover all the seeds and then some.

Anyway, I like to do at least 3 boils, but 5-7 will ensure that you get most, if not all, the goodies out. I usually combine all boils at the end and reduce to approximately 1L of rue tea before beginning the first basing step. But they may just be me!

Good luck!

Moral of story: take Imodium before extracting

Have you checked The Tao of Rue Extraction?