VL6180x sensor breakout stays on despite removed VIN
So that's just a breakout board for this? http://www.st.com/content/ccc/resource/technical/document/datasheet/c4/11/28/86/e6/26/44/b3/DM00112632.pdf/files/DM00112632.pdf/jcr:content/translations/en.DM00112632.pdf

If so, you can hold the GPIO0 input (the 0 on the breakout board) low to put the chip into a reset state. This means you will need to dedicate an I/O line to each board, but that way you can bring them up one at a time without doing crazy things to the I2C bus itself.