Transposition mysteries

I recorded my original project (drums guitar, lead guitar) at 44100 24 bit on a tascam 2488 . I imported the project into sonar 5 a year ago using the original bit option. since then I upgraded to sonar 7. I did all of the vocals and bu vocal fixed up the guitar and drum tracks and it sound's great. However when I went to add the bass lines the bass sounded out of tune so I checked and rechecked and the bass was dead spot on the intonation was also perfect. I checked my recoding in spots using the v vocal and Antares auto tune and realized that the original recording was now in Eb not E. So I audio transposed down the bass part and it integrates nicely. I am working on the organ part and I need some more lead fills. I tried to transpose the original part up a half steps and ouch the sound was something awful the drum went all out of sync. Time is an issue and I do not want to go back to rerecording from scratch. Currently I am hoping the guitarist can just add his parts and I can just audio transpose it down and it will work like the bass did. I am going to mix down what I have and try to audio transpose the mix up a half step for this. Has anyone else run into this issue? How do I prevent this from happening in the future?