Yes, as long as the timing requirements are met. The easiest way to change sequencing modes, to higher or lower resolution, is to do it at the HOME position (HOME is low). Otherwise, when going from a lower resolution to a higher resolution mode (half-step to quarter-step, etc.) both sequences have identical output currents. (Both sequences fall on the same row of table 2 in the datasheet.) The translator will keep the output current levels unchanged until the next step, at which time it will begin the smaller steps.
To keep the motor moving at a constant speed while changing sequencing modes, the step frequency must be multiplied by 2, 4, or 8, depending on the modes you jump from and to. Going from a higher-resolution mode to a lower-resolution mode should only be done when both modes appear on the same row of table 2 from the datasheet (Eighth Step #5 and Full Step #1, etc.). This is only important if position must be maintained or if there is no position control loop.
It should be mentioned that changing the MSx pins at any time will not cause damage to the device. To keep the motor moving at a constant speed while changing sequencing modes, the step frequency must be divided by 2, 4, or 8, depending on the modes you jump from and to. If you go from a higher resolution mode to a lower resolution mode and do it at a position that is not a valid possibility for the lower resolution mode in table 2 of the datasheet, then the sequencer will advance to first possibility without actually changing the output currents. When the next step arrives, the device will go from the position the translator was at before the sequencing mode was changed, to the next position of the new sequencing mode. For example, with direction low, if you changed from Eighth Step mode to Full Step mode when you were at Eighth Step #2, the translator will advance to Full Step #2 (but not change the output currents). When the next step occurs, the position will go to Full Step #3. The effect would be that the motor would move by 11 eighth-steps. This would make keeping the motor at constant speed very tricky.