I am not sure I understand that question. You exchange eacute.001 for eacute.002. Why would that not work?
Have you read Features, part 3: advanced contextual alternates | Glyphs?
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I’m just imagining managing these huge groups of glyphs. 
A handwritten font lives from variations, and if they all have marks… Man, I’ve got some work to do.
Efficiency pro tip: If you have a, a.alt and acutecomb, and you generate aacute and aacute.alt via Glyph > Add Glyphs (Cmd-Shift-G), Glyphs will automatically compose aacute from a and acutecomb, and aacute.alt from a.alt (!) and acutecomb. IOW, Glyphs is looking if the components are available with the given suffix.
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You’r tip came right in time. I’m starting to build the OT features in the next days. I’m looking into setting up (sub) groups and have to build a structure to make this work. This is the first time I’m doing these complex features like LIGA, CALT and SWSH. I want to do it as clean and effective as possible, avoiding rendering glyphs or groups not functional.
If you know of any good reading material I’d love to hear it. It’s a steep learning curve, but I’m game. 
Rainer: I’m looking to create something similar to your Sephora Script font. The way that ‘dances’ when you type is the OT features I’m looking to create. 
We had special Python scripts that were generating the feature code for those. And it became very complex eventually.
- Learn Python, tutorials are available. Peek into my scripts to see how you can add OT feature code.
- Learn OT feature code in and out. Tutorials and Tal Leming’s OpenType Cookbook should contain nothing new to you.
- Keep ligatures to an absolute minimum. You want to avoid ligatures with marks.
- Start with the positional features (tutorial available), add subsequent features in separate lookups afterwards.
- Create medials that connect with a following n and similar letters (b, h, i, j, k, l, m, p, r, t, u, y), YMMV.
- Then focus on the substitutions based on the following letters, create letter groups with a special suffix, e.g.,
.efor all letters that connect with a following e (and other letters with a similar round shape: a, c, d, g, o, q and their diacritics). - Some letters will not connect. In a new lookup, substitute letters based on previous letters if the don’t connect.
- You will have problems with r and s. You will have to deal separately with those, or find a solution like Victoria Rushton has, see her appearance in the Typographics 2016 video (you should find that on Vimeo, I think).
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