3 Phase PMSM Motor Current Measurement: Figuring out the 2 negative terminal currents with 1 positive current measurement
Remember how Space Vector Modulation works. Every PWM cycle inverter switches between two active voltage vectors (\$v_1\$ and \$v_3\$ in this particular case) to synthesize the reference vector \$v_{ref}\$. The two zero vectors \$v_0\$ and \$v_7\$ are also used to add dead time to the switching pattern. This dead time reduces the voltage magnitude and is necessary when the voltage reference magnitude is less then 100%.



The zero vector \$v_0\$ corresponds to a configuration when all low-side switches are ON and all high-side switches are OFF. The \$v_7\$ vector is the opposite of \$v_0\$ and corresponds to a configuration when all low-side switches are OFF and all high-side switches are ON. Since you said that your H-bridges have their current sensor at the high-side, you should measure the currents when the \$v_7\$ vector is active.

Honestly, I have never tried this scheme, but it sounds pretty reasonable. The only thing is that you should carefully synchronize your ADC and PWM hardware. Hook up an oscilloscope and look at the current transients when switching between vectors. Most likely, the best time to take the measurement will be at the middle of the \$v_7\$ vector.

For more information you may google for the "Three-Phase Current Measurement" PDF from Freescale (now NXP). They do the same thing except that they have their sensors on the low side. Hope it will help.