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A few questions about sanitation and shelf life.

(To make it easier to pick out my questions, I've put them in bold below)
 
I made my first hot sauce last month using jalapenos, onion, garlic and golden raisins.  Ultimately I loved the flavor, but it was a little thick (it was hard to get in and out of the bottles) and it was also not quite spicy enough.
 
I followed some sanitizing instructions online using a boiling method.  I boiled the bottles and caps for 15 minutes, I filled the bottles up with still-warm hot sauce, then I boiled the bottles again for 10 minutes.
 
However, I think I made a mistake because the bottles I got had a little paper flap in the cap.  I read later that you aren't supposed to boil them.
 
I'm going to make a second attempt at this recipe to try to fix the last batch's shortfalls and I have a lot of questions.  I was going to add more water to the cooking process (since the raisins sucked it all up last time), use a blender instead of a food processor to try to get it smoother,  and I'm going to use a pH meter and extra vinegar and/or ascorbic acid to try to make it "shelf safe."  I was also going to add a single habenero to the batch (of 20 jalapenos) to try to get the heat level up.
 
So my first question is, If you accidentally boil-sanitize a cap with a paper lining in, how does that affect how safe the sauce is to eat, and for how long, provided it is kept in the refrigerator?
 
My next question is: What is the best way to sanitize a bottle with a paper lining in the cap?
 
Also: How long will a properly sanitized bottle of hot sauce last unrefrigerated on the shelf if the pH level is 3.5?  Is this a good level or should I try for something lower/higher?
 
Finally: Will using a blender instead of a food processor make my sauce smoother?  Are there any other methods besides adding a liquid to smooth out the sauce?
 
Thank you all for your expertise!
 
Greetings, gilgatex and :welcome:
 
In case you haven't found the Making Hot Sauce 101 thread, most of your questions should be answered there.
 
 
 
So my first question is, If you accidentally boil-sanitize a cap with a paper lining in, how does that affect how safe the sauce is to eat, and for how long, provided it is kept in the refrigerator?
I would be worried that water could have gotten under the cap during the boiling process and compromised the paper liner, which in turn could compromise the seal and safety of the sauce if left unrefrigerated.  The sauce could be kept refrigerated...or it could be re-processed.
 
​2 ways to re-pack-
​a- dump all the sauce back into the pot, reheat the sauce, wash the bottles, then follow the hot fill/hold processing from HS 101.  Since you are not happy with the consistency, this is a way for you to address that issue as well.
b- remove the cap and liner.  Place the filled bottles in a pot with a wire rack on the bottom.  Add other bottles or jars to make sure the bottles can't tip over. Fill the empty jars with water so they don't float.  Fill the pot with water up to the neck of the sauce bottles and bring to a simmer.  Keep at a simmer until the sauce in the bottles is 195-200F.  

​Once the sauce is hot, turn the burner off so the water isn't actively boiling, remove each bottle and immediately cap with a New Cap and invert.  You may want someone to help holding the bottles upright while in the water.
 
My next question is: What is the best way to sanitize a bottle with a paper lining in the cap?
​No need to sanitize the cap, follow the instructions in HS 101
 
Also: How long will a properly sanitized bottle of hot sauce last unrefrigerated on the shelf if the pH level is 3.5?  Is this a good level or should I try for something lower/higher?
3.5 is a great pH level.  A properly packaged sauce will last...pretty much indefinitely if it isn't subjected to extreme heat or cold.  It may have some color change, but if the pH is good, the sauce should still be safe to eat.  Some canning websites say to use canned foods in 2 years.  A lot depends on what is in the sauce. 
 
 
Finally: Will using a blender instead of a food processor make my sauce smoother?  Are there any other methods besides adding a liquid to smooth out the sauce?
 Liquids aren't that bad, think of maybe using juice instead of water or vinegar.  Also, a food mill will remove some of the pulp.  
 
​You can buy caps individually from most bottle suppliers for pennies, so don't worry about having to toss away the first caps and using new ones.  
 
Good Luck and Have Fun!
SL
 
 
 
 
 
 
 
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