TMS320F28035: Switch from internal crystal to external

But two boards don't work again after remove C45, C46 and solder back

If the boards were working earlier and are not working now after replacement of C45 & C46, I suspect the following: Incorrect capacitor values or damaged solder pads. Or there is some marginality in the design (crystal parameters and/or the load capacitor values) that prevents it from consistent operation.

I can see it has 20MHz, 1.8V sine wave on crystal pin, is it meaning that there is no problem on crystal？

If you see oscillations, it is likely that the oscillator is oscillating. Can you compare the magnitude of oscillations with a good board? That will provide some indication on whether the series resistance is too high and making the oscillator design marginal. Also bear in mind that the very process of connecting an oscilloscope probe to the X1/X2 pins could affect the oscillator operation, unless you are using an (active) FET probe with a capacitance of < 2 pF.

Could you kindly help check the SCH below and crystal spec? It seems the ESR of crystal is a little high but still in the range of 30-150 Ohm.

We may be able to provide some overall guidance, but we are unable to provide definitive recommendations. That is the reason we have the following note in our datasheet: TI recommends that customers have the resonator/crystal vendor characterize the operation of their device with the MCU chip. The resonator/crystal vendor has the equipment and expertise to tune the tank circuit. The vendor can also advise the customer regarding the proper tank component values that will produce proper start-up and stability over the entire operating range.