H-1B cap subject petition after consular approval

[avsk]

I am an F-1 student, OPT started June 2018. Company A applied my H-1 COS and it got picked in May 2018. However I did not join A. They requested USCIS to withdraw my petition after it got approved in September 2018, before the change of status took effect. Company B where I joined applied for a H-1 transfer based on previous approval and the transfer got approved in June 2019 while the withdrawal was still pending. USCIS finally sent withdrawal for A's petition in July 2019. 

However, my company B is not inclined to activate the newly approved consular H-1B. They say that the previous H-1 was withdrawn before it took effect and that I would face issues in future USCIS applications. 

Can my employer B, apply for H-1B under cap subject again in 2020 without withdrawing their previous consular petition or while the withdrawal is pending? Will USCIS process the new I-129 application?