Misunderstanding maybe but VNA calibration and actual measurement setup calibration are two very different things, and you have not done measurement calibration?
Measurement calibration is a must to be done if it is a complex and unknown load between VNA and actual measurement object.
A complex loss involving several loss-factors causes amplitude and phase values that varies with frequency in a non linear way.
Calibration which includes compensation for complex losses near measurement object can be done in several ways and depends a bit on type of calibration procedure that actual VNA can handle.
Method resulting in most reliable result is in my opinion in place calibration, Short Open Load, and manual setting of correct electrical delay if it not is a part of standard calibration procedure.
If losses are purely real and not causing any phase delay can a fixed scaling factor be used.
If losses have low impedances will it make calibration less precise, due to VNA dynamic limitations. Most simple solution is to cut PCB traces that connect these lossy parts during measurement and measure that part later, if needed, to get the whole circuit status.
For low frequencies and short measurement distances relative wavelength can maybe both phase and component losses be omitted or replaced with their theoretical values.
If lossy part complex values are known, as an S11-parameter table, can these be subtracted from S11 measurement. Problem is that without calibration can not either the losses be defined.