welcome to the forum.

(leica raw data has all the distances with scale 1.000)but the scale in the area of the network is 0.999635

Usually, the scale of the atmospheric compensation is applied to both, the slope distance and the horizontal distance. Moreover, the scale of the projection is - if any - applied to the horizontal distance, too, but not to the slope distance because this scale ist not defined for slope distances.

Your scale looks like a UTM scale and must be applied to the horizontal distance (GSI block 32). If this scale was not inserted to the instrument, you can apply a scale within the adjustment. The following screenshot depicts the setting panel of the distances. A scale is estimated wihin the adjustment, if the checkbox is checked. If the checkbox is not checked, as seen in the screenshot, the ppm-value given in the textfield is used as a deterministic correction value. The default value is 0 ppm, so no further scale is applied.

According to the documentation, the functional model of the horizontal distance reads
$s_{2D} = \frac{1} s \left(\sqrt{ \Delta x^2 + \Delta y^2}- a \right)$
where $s$ is the scale and $a$ is the zero point correction.

Kind regards
Micha

Thank you in advance.