Once Dept. itself granted registration of two different firms at the same premises, it follows that receipt of goods between these firms can happen without any movement of goods (presuming that goods were lying in the premises at time of sale between these two entities).
In addition, 'receipt' of goods need not be only be physical-receipt but also it can be symbolic / beneficial / held-in-trust. One can delve into 'explanation' given under Section 16 (2) (b) of the CGST Act, 2017 as well as Section 10 (1) (c) of the IGST Act, 2017.
Of-course, creation of "fake" e-way bill/s has made your case suspicious. One should admit the mistake (presumably, by seller) in creating these e-way bills unconditionally but explain your position with various documentary evidences such as stock register, bank statements, ledgers, CA certificate & so-on (along-with affidavit from seller) and defend ITC using all available evidences & legal provisions in support.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.