This is a well-known limitation that unfortunately is not mentioned in Help
for either the ATP Regression tool or for the LINEST worksheet function which
performs the core calculations.
If you are doing simple linear regression, the SLOPE, INTERCEPT, RSQ, and
STEYX worksheet functions do allow blank cells in the data range. If you are
doing polynomial regression, the trendline option for the "XY (Scatter)"
chart can calculated the fitted coefficients and the R^2 (though you will
probably have to format the output to display more figures).
Jerry