Dear Eric, Rachel, Giulio, Douglas and Yifan, 
Thanks for all the ideas and questions!
Here is the summary from all what you asked and wrote. If I am doing something wrong by posting in here, please let me know. I rather place all the info for other that might have seen something similar or will see something similar in the future. The more brains, the better :-) 

Answering all your questions to expand the information. 
- Strains used: B2086 and CU428.2
- Origin: Prof. Josef Loidl
- Mating protocols used: Same as from Josef, only difference is the source of peptone/tryptone (in my opinion)
- Centrifugation: max. 196g in a swing rotor (around 1000 rpm)
- The mating was working fine about 6  months ago, they just stopped now.
- "Does cell lysis occur after you mix the two strains?" Cell lysis takes place before they get mixed or sometimes after they get mixed. I am suspecting just the length of time in starving media, but it is an interesting question... I will pay more attention before I give a final answer.
- The culture is axenic at the moment. I read that choanoflagellates are driven into sexual mating by Vibrio fischeri, so we are doing some experiments to see if the strains will recover their mating behavior after being fed with live bait. Kind of stimulating their predatory instincts again. We will see what happened after the holidays. I will keep you updated

Ideas you all gave me:
 
1. "One is that you may be harvesting you cells at to high of a g force. That can trigger lysis or mucocyst discharge. It can appear as cells lysis but really is just a lot of protein secretion." - THAT IS SOO COOL!. I will look in more detail, but based on my previous observations, they do look very similar to NETosis I have observed in neutrophils. Do you think I will be able to distinguish one from the other using DAPI staining?

2. Change the Starving media from Tris 10 mM to Dryl’s medium.-  Thanks. I will get right onto it.

3. Cells might be lazy (or tired), get a new set - Yes, I am working on it. One from the community has already offered to send me a new set :-)

4. "Check contractile vacuoles and food vacuoles in your Tetrahymena cells.  See if there are any anomalies." - Like, just visually or with some kind of test? Sorry, very new here with the little ciliates.

I hope I addressed all questions. Thanks again!
Happy End of the Year time!
Luisa