I found an excellent website
with information about restoration projects at popular Japanese tourist spots, including the following World Heritage Sites:Ancient Kyoto
: Kiyomizudera Temple has restoration projects under way that are expected to be completed in 2019
. Currently, the Okunoin Hall, Amida Hall, and Shaka Hall are being renovated
: The East Pagoda at Yakushiji Temple is currently being renovated and is covered by scaffolding; the restoration should be completed in 2019
: The main hall at Rinnoji remains enclosed by scaffolding, but remains open through its restoration, which is expected to be complete in March 2019
. Also, the prominent Yomeimon Gate at the Toshugo Shrine is also undergoing restoration and covered by scaffolding; this restoration is also expected to be complete in March 2019
I'm not including the Peace Memorial Museum renovations in Hiroshima since the Genbaku Dome is still accessible.