First of all, wind load in BNBC-2020 is a service level load, that’s why we multiply wind load case by load factor (>1) to get Strength Combination.
But earthquake load is a strength level load, that’s why we multiply earthquake load case by load factor equals to 1.0 to get Strength Combination.
BNBC-2020 clearly states in section 6.1.10.2 that for strength level load analysis, cracked section properties as specified in section 6.3.10.4.1 (a) to (c) need to be used.

Figure: Stiffness Factor guideline for lateral deflection under earthquake load
By factored lateral load BNBC-2020 indicates Earthquake load here.

Figure: Stiffness Factor as per section 6.3.10.4.1
Again, for lateral wind load, BNBC-2020 gives the following guideline for considering stiffness factor.

Figure: Stiffness Factor guideline for lateral deflection under wind load
Here BNBC-2020 suggests to check section 6.1.11.2 & 6.1.11.3, but nothing is mentioned in those sections about member stiffness.

Figure: Referred section by BNBC-2020 for member stiffness (1.4 times) under wind load
In this situation the understanding of author is that, BNBC-2020 is referring to section 6.3.10.4.1 actually which can be confirmed by international codes (such as ACI 318-14).
ACI 318-14 elaborately explains about section stiffness properties in section 6.6.3.

Figure: Effective stiffness factor for factored load analysis and earthquake lateral deflection check (ACI 318-14)
For service load level analysis and to determine deflection under service wind load ACI 318-14 gives the following guideline.

Figure: Effective stiffness factor for service load analysis and wind lateral deflection check
(ACI 318-14)

Figure: Effective stiffness factor for service load analysis (Table taken from the article published in Structure Magazine, ASCE 7-16 Provisions for Lateral Drift Determination by Abdulqader Al-Sheikh)
Therefore, it can be summarized that, for design USD load combinations and for checking lateral displacement for earthquake load section properties mentioned in section 6.3.10.4.1 of BNBC-2020 shall be used. However, it is to note that deflection amplification factor Cd shall be multiplied with the displacement obtained for earthquake loads using those stiffness values.
And for design with ASD load combinations and for checking lateral displacement for wind load, vertical deflection of beams, slabs etc. section stiffness shall be 1.4 times of the stiffness mentioned in section 6.3.10.4.1.