What do they fill root with during endodontic procedure? any connection to blood supply?

Gutta percha: For years the filling material has been gutta percha with different types of cements. Some of the cements are not resin based.

Gutta percha.: The canals are filled with a material called "gutta percha" which is made from the sap of trees native to southeast asia. The material is similar to rubber or latex but is biologically inert. The gutta percha is either warmed when placed or compacted mechanically at room temperature and is used with a liquid sealer. There is little, if any, contact with blood after it is placed.

Gutty perchance: Most commonly a rubbery material called gupta percha is used to seal the canal system with a sealer. ( resin or non resin based). All of this material is usually confined to the tooth and should it be connected to the blood stream. Over filing a tooth could have some blood contact. Many years ago some teeth were filled with silver points, this is no longer routine practice.