Tempo change using flextime (with different time signatures and tempos) difficulties

I am re-recording the vocals on some unfinished projects from a couple of years ago.  One song is recorded with various changes between several different time signatures, each with different tempos (The verses are in one time signature and tempo, the chorus in a different time signature and tempo, the bridge in different time and tempo again, and then there are a couple of transition bars between 2 different parts, with the tempo slowing down or speeding up...) All these changes are set up in global tracks.  I've now realised the verses (and possibly the bridge) are just a few beats too fast, while the rest of the song is fine.  After watching a few YouTube videos, I worked out how to apply flextime with polyphonic mode, changing the selected times in tempo under the list editor.  I started with one track, and then one by one applied the polyphonic mode to each track.  The four guitar tracks are all perfect with the new tempos.  However the bass and the drumkit go out of sync at different moments.  Namely the first change  from 5/8 (110bpm to 106bpm) to 4/4 remaining at 124 bpm (chorus) - the drums are out for the first bar which transitions into the chorus, and then fine again, while the bass is out for the transition and entire chorus.  The second verse is all working fine again.  The drums are almost perfect on the transition into the chorus, but the bass goes right out again for the duration of the chorus. Everything rectifies on the transition (5/8) into the bridge (7/8 at 122bpm, down from 124).  The bass stays good this time for the bridge, and remains fine for the transition back to the chorus and for the outro, while the drums go out in the transition to the final chorus (and then are fine again).  I've saved the changed tempo version under a different name, so still have the original version.  I've noticed that the positions are the same (in list editor tempo) of both saved versions, however the SMPTE positions are different.  Unsure if this is of relevance. Is there anyway to rectify this problem?  I don't have the time or resources to start again from scratch, and it is just that bit too fast to sing in the verses.  I have Logic Pro X Version 10.3.2 on Macbook Pro 10.11.6.  Thank you for any suggestions! Edited October 17, 2017 by StartingOut

Have you considered using Q-Reference, Group editing feature, groove track and/or groove template?

SMPTE is timing reference usually related to movie/video/audio syncing.

SMPTE-locking is a way to edit unlocked items against locked one (latter remaining locked to the absolute time reference). Perhaps, it is something that is unrelated to what you describe. The discrepancy SMPTE settings between the two versions should not pose problem.

Thanks for reply!  I'm just a beginner in all of this, and in the research over the past few days I am thinking that the bass should be monophonic and the drums rhythmic, though that hasn't made any difference.  I have just watched a YouTube video on groove track, but thought that might apply better to drum loops (my recording is with live instruments)?  I will certainly give it a go.  On closer inspection, I have noticed that where they go out of sync, the bass (and I presume the same with the drums) has skipped a part of the recording.  e.g. As I transition from 5/8 to 4/4, there is one extra bar of 4/4 -  the last 2 quarter beats of that just disappear from the audio playback.  On the soundwave, up until the end of the extra transition bar of 4/4 is still there, however the last 2 beats are blue (instead of white).  The chorus then commences with a different take (take 4).   The first take stopped at the end of the transition bar in which 2 beats have disappeared... I hope that makes sense!  Then when it goes back in sync again after the chorus, there are actually 2 beats of silence.  So that explains why it is in and out of sync, now I just have to work out how to get the missing beats back.  I'll look into groove track and your other 3 suggestions (that I have to research up on tonight).  I'll play around with it to see what I come up with, and will keep you posted! Thanks again! Edited November 21, 2017 by StartingOut

Thanx for sharing your experience!