Is this service adjustment done mechanically (potentiometer on the PCB,...) or by a software adjustment with a special proprietary tool?
The adjustment can be easily applied by post-processing the samples in the digital domain, so likely no analog circuitry is involved.
It should be easy for the self-calibration procedure to determine the necessary gain and offset values for aligning the ADCs, so in fact I would be rather surprised if this would require a factory calibration (but who knows
)
I take it for granted that you did not forget to run self-calibration, did you?
Here is the full spectrum with a 4.5 MHz sine (FFT in dBVrms):
So you're facing a SFDR of about 34dB, or maybe a little bit more, since the sine wave amplitude was not full-scale yet.
The handbook specifes SFDR >=40dB (but it does not promise significantly more either).
[ Just for comparison the typical SFDR including inverleaving spurs for the HMCAD1511 (which is used in the SDS1000X-E models and also in some other DSOs in this class): 44dBc in dual Ch Mode @500MsPs, 49dBc in single Ch Mode @1000MsPs, and 57dB in quad Ch Mode @250MsPs. ]