The reason a chapter stays at 1000 (or there about) is because it's the rules given to them in the Codex Astartes. It's not that they don't have enough to make more marines, it's that they aren't suppose to. The Black Templars are several thousand strong and this is getting them attention from some inquisitors who fear the power the Grand Marshal wields.

Also, I don't think it's possible to get back all the gene seed, some would get let on fire, blown up, lost in space, eaten, or just abandoned in an embarrassing defeat.

 

hmmm, I suppose I should've worded that differently. I know they aren't allowed to have more than 1000, but I wanted to know what happens to the leftovers.

And thats actually why they have 2. The one in the chest is much more protected under power armor, fused ribcage, 3 lungs, 2 hearts, dense muscle, black carapace, etc. I believe the one in the throat is the one they usually try to harvest first, as it is faster.

 

I believe they send some as a tithe to Mars to check for genetic deviancy as well as to help found new chapters - they have to get their geneseed somewhere, after all. I'd imagine most of the rest gets kept in cold storage in case of the aforementioned embarassing defeats - if you lose 500 marines and can't recover any of their geneseed, that's going to hurt a lot.

 

Also, the progenoids take a human lifetime (give or take I can't remember exactly) to mature to the point where they'll give viable geneseed. This means if a marine dies too early, his geneseed is wasted.

I seem to remember they're both in the back of the neck, hence why an apothecary has that drill-thingie to extract them quickly in battle. So yes, they could feasably be destroyed.

Finally, marine chapters are expected to tithe a portion of their harvested geneseed to the Adeptus Mechanicus for monitoring, and for the creation of new chapters.

 

Redundancy - because the Emperor knew that Space Marines aren't nearly as immortal as he would have liked others to believe!