In the case of Amaj7, Dm7b5/F#, Bm9, E7b9, the progression is chromatic, but the obvious tonal center is A, and the progression sounds like a major progression, so you can use A Major over the whole thing. Another way to look at this is stripping the chords of all their extensions. This leaves you with A, Ddim, Bm, and E. The D diminished can be seen as a substitute for G# diminished. Now, you have A, G#dim, Bm, and E. This correlates to A Ionian, in modal terms, once again allowing you to use A Major for the whole thing.

For the progression in my earlier post, Am, E/G#, G, D/F#, F, E, one can see the progression as a combination of chords derived from the Natural, Harmonic, and Melodic Minor scales. A Natural + Harmonic + Melodic Minor = A, B, C, D, E, F, F#, G, G#, so you can use A Aeolian (A Minor), or A Harmonic Minor, or A Melodic minor for lead over the whole progression.

But, once again, use your ears as the final judge of what you should do or not. Listen for the tonal center, then listen to see if the progression sounds major or minor or diminished (diminished tonalities are rare), then just use modes based on that tonal center and tonality. If the progression sounds major, and the tonal center seems to be A, try out A Lydian, A Ionian, and A Mixolydian (or A Bebop). If you want to stay safe, you can use A Major Pentatonic, because it doesn't contain the 4th or the 7th (which are the two notes that change between the major modes). If it seems minor, try out A Dorian, A Aeolian, or A Phyrgian. A Minor Pentatonic would be safe, because it doesn't have the 2nd or 6th, which are the two notes that change between the minor modes (you can also use the A Blues Scale). Finally, if it sounds diminished, use A Locrian, but this will rarely be the case.