Here's some research that claims flossing actually causes problems.
"Dental flossing can produce bacteraemia in periodontally healthy and periodontally diseased individuals at a rate comparable with that caused by some dental treatments for which antibiotic prophylaxis is given to prevent IE." http://onlinelibrary.wiley.com/doi/10.1111/j.1600-051X.2008....
But in general, interdental flossing is very good against contact cavities [1]. Perhaps deep flossing is leading to bacteraemia. I have always found hard and awkward to perform deep flossing, and that's why I use oral irrigators instead. However, maybe irrigation also leads to bacteraemia. I've seen some references supporting that too.
If your mouth has an unhealthy microbiome, you might need to place a lot of emphasis on killing bad bacteria initially. For this purpose, salt water or mild antibiotics (chlorhexidine) for 2 weeks combined with double dose of probiotics should do the trick.
Obviously, sugars feed bad bacteria, which metabolize it into acids to erode your enamel. Avoid entirely.
Flossing is an obvious way to disrupt pathogenic bacterial colonies by abrasion. I think irrigation is much better, as it reaches deep pockets below gums. But it doesn't replace flossing entirely.
Those two, coupled with regular brushing of teeth, gum and tongue, plus oral probiotics should keep issues at bay.
In particular, my experience with probiotics is that tartar calculus fell apart within a few months. I have never had a cavity.
Sadly most dentists don't place too much emphasis on these as it goes against their business model: drill, fill and bill.