Poor hygiene will lead to tissue infections, bleeding when flossing, bone loss, etc--the list goes on & on. So yes, improper hyg. can cause pain! Perio patients can attest to ongoing, constant, nagging aches = )
*If* the root is fractured, that is a constant 'wicking' of infection & bacteria traveling along the length of the fracture, causing inflammation--so I can understand why it's uncomfortable to floss there. Try some warm salt water rinses, mix a bit of peroxide in as well, that'll help bubble out any debris that my be stuck & adding to the tenderness. That may help with the discomfort some (jeez...yes--we were taught to use the term "discomfort"...but you know, when I've had toothaches, it's called "DA*N PAIN"!!)
If your gecko is broken, you have a reptile dysfunction.