Audio in team project sequences out of sync - audio starting from beginning at every cut

We have run into a big issue with a team project. Two people were working on multiple sequences that were synced with external audio tracks. When another teammate published their work, the audio in my timeline went out of sync, where the audio track started playing from the beginning in every cut, instead of its cut point. (tried offlining and relinking several times). The original sequence where I synced the audio is still in sync so it appears sequences where I made edits just forgot where the ins/and outs were for each cut. Is there any way get Premiere to remember the cut pionts? 

Some of the audio tracks had the same names from ie. ZOOM001but were located in different folders. Not sure if that scrambled up anything.