I hear you on this, and have brought this issue up before.
My least favourite part of Construct2 is the project management aspect of it. I would ideally like to save iterations of a project with a "save as" command within the project folder structure, so all project files relate to the same project assets.
Also, the current method of swapping out and appending animated sprites is a nightmare! To import an animate sprite, I have to import the first frame into the sprite editor, and then right click the animation window to import all, except the first frame. Why can't I just import all animate frames at once?
If I need to replace the animation, it is possible to replace them in the folder and then update but I have found it to be flaky as you have mentioned. Also, since Construct has changed the naming convention, so it is now 000.png 0001.png etc it means I need to re-render out my new sequence to this , instead of something meaningful like alienwalk000.png.
It is also impossible to multiselect more than one frame of animation to delete before replacing them. We really need an replace all frames function in the sprite editor.
My current workaround is to rename the animation I want to replace (for instance "walk" becomes "walk_old")Then create a new sprite animation called with the old name("walk") and then import the new frames. Then delete the original sequence("walk_old"). I have found that this works better than replacing frames in the folder structure, but it is clunky!
Hope to see some love put into this in the future by Scirra <img src="smileys/smiley1.gif" border="0" align="middle" />