The recepient vector has a already got two genes in it example say geneA and GeneB. Linked with P2A. i wanted to remove Gene B from the vector and replace it with another geneC. And removing geneB alone is not possible because no restriction site present. one way to excise geneB is by restricting it with site available in Gene A at its  3'end. if i use restriction site of Gene A at 3, end , geneA will lose 100bp at its 3' end. In that case whether Gene A can express protein. My major aim is to make virus after cloning. 

One solution is i can replace it by adding linker , but can linker be synthesised with 100bp long? i am not planning for PCR amplification and cloning.

HELP ME!!