Very simple workaround at the moment. Disable Bottleneck, activate unDecorator, after saving game, swap them back. Doing this disables replay though... no biggie unless you have a mod that adds a lot of ores or something.

This is not something that should be handled by the Bottleneck mod. unDecorator blindly deletes entities from the map, including the indicator lights from the Bottleneck mod.

it seems to be a problem with the intentions of those two mods:

undecorator removes everything without a function (all decorations) to make a map take less space (in memory as well as in save files, eg reducing my map from 240 MB to 95 MB and time to autosave it from 20+ seconds to 5 seconds), and when bottleneck adds its marks it seems to do so by adding decorations to the map. how should undecorator know that those decorations are wanted by the user ?

to automatically solve the conflict, either undecorator would have to add checks to not remove some decorations (which requires lists of decorations to be added as some kind of whitelist or blacklist and which multiply its cpu usage), or bottleneck doesn't add its marks as "decorations" which by definition are "only decorations with no real purpose".

but as far as i have seen, undecorator removes decorations only in two cases: when a "fullclear" was not yet done, it (once!) removes all decorations from the entire map (thus the above workaround should help to initially clear the map once). and it removes decorations from newly generated chunks (which don't have any machines yet, thus no problem).
if you install both mods at the same time or start a new map with both mods active, or if you install bottleneck later on a map which has undecorator running, i see no reason why there should be a problem at all. removing "the wrong" decorations might only happen when installing undecorator after having run factorio with bottleneck only.

As Anson points out, there shouldn't be a problem, if unDecorator is running from the beginning of the game.

To handle this problem itself, the Bottleneck mod would have to perform many checks for every single game tick, just to see whether some other mod had decided to delete (some of) its decorative entities, slowing it down tremendously. Currently, decorative entities are the only entities that support render_layer, which appears to be necessary to get the indicator lights drawn correctly. unDecorator's fullclear is basically an "rm -rf *", which is going to clash with every single mod that uses decorative entities, and not just Bottleneck.

Thanks for info. As I'm sure you realized, that I did find it, and then add it to a running game. Will add it to list right before starting a new one, so I won't have that problem.

Really, really like your mod... very helpful. Are you planning on updating the photos to show the new indicator location?

I didn't realize that the indicator location had changed. Aren't they in the same place as before?

Here is a working fix that patches the undecorator mod so it skips the bottleneck stuff: http://lappro.net/files/random/undecorator_1.0.3.zip

Already opened a discussion there so the author might include it in an update.

P.s. this discussion should've been marked as a bug.

I've just uploaded a new version (0.3.3), which should fix the compatibility issue with unDecorator.