Can reagents between QuantSeq FFPE and QuantSeq V2 kits be exchanged?

No. QuantSeq FFPE and QuantSeq V2 protocols use different reagents and volumes for the library generation. Please see the following FAQ: What are the differences between QS FFPE and QuantSeq V2 kits?

However, the reagents for PCR amplification are the same and, therefore, are interchangeable between the two library prep kits (PM buffer and PE enzyme).