I just sat down to try to replicate what you described, and I cannot. I took a single vocal track, threw in GR5, another FX chain, and did a region FX on the entire clip (30 seconds).
Next, I cloned the track, the Melodyne edits did
not copy, and the "view" of Melodyne shifted as well (from basically 2 octaves to almost a "fit to window mode"). I then removed the region FX, FX chain, two other effects, and finally GR5. I did not have an issue doing this. I did not get the "blank synth" slot either.
The issues I have been having with Melodyne (and some are posted) when using in
ARA mode:
1) Edits do not save when a project is saved (although I think a couple times it did, but is not "reliable")... there is a thread on this.
2) Cloning any track with Melodyne in the Region FX does not clone the Region FX.
3) Melodyne always initially tells me I need 1024 samples for the buffer (which I do), but this then goes away as long as I do not close SONAR (i.e. I only get this on the initial Melodyne instance after SONAR is opened). I can close/open projects, etc. and not see this message again as long as SONAR remains open.
4) Melodyne shifted its default view in the cloned track. However, I did not delve deeply enough to see "how much" is different.
As I put in another thread, ARA sounds awesome in theory, but there is a lot of handshaking needed to make it "seamless," and to me it is not.
Flip side to this... Melodyne Editor functions "as designed" in stand alone mode... but in ARA mode it has gaps that limit its usefulness.
Michael