When you delete a clip, Premiere should not delete all instances of it in all sequences

Yup. Premiere is trash when it comes to media management. And the longer the team avoids redoing the entire media structure of the application the worse it will get. They have stretched an old pro-sumer level tool as far as it can go into the professional realm.

Your example regarding clips vs sequences is a golden example. The sequence should reign supreme as an infalable database of all it contains. Much like the way an EDL would refer to it's source media. It needs to be a permament record. If you delete a clip in the project window, it's former place in the sequence MUST REMAIN! This is how it is in Avid Media Composer and etc. 

It is far too easy to jack up a project in Premiere.

The next rung of WTF is Premiere not understanding the relationship between subclips and masterclips. Not just in match framing back. But when consolidating, archiving, and restoring old projects the applications doesn't remember numerous subclips came from the same masterclip and treats each one as a new separate piece of media and duplicates the referencing source "finder" level media file numerous times, CHANGING IT'S FILENAME to allow the duplicates. This is a DISASTER.

Well Adobe, what say you? Gonna try to twist this as an intended feature? Or admitt this is a mess and try to fix it. 

ok now this problem has gotten worse.  when u delete a file in premiere there is no warning that the file is being used.  and it just plain deletes it from all sequences.  This warning needs to come back adobe!

AGREED that Premiere does not have the most efficient media management. Editors are stuck with gigantic projects that become slow because there's so much redundancy. The beauty of Premiere is that editors can import sequences from their AEs but the "not so beauty" is that all the media associated with the imported sequence gets copied again into the project. I did Kevin's suggestion but I still can't get rid of clips without deleting them completely.

Hi Bill at Radley,

It sounds like you are frustrated with projects that you've inherited that display unexpected behavior. Sorry about that. That said, we are not a part of the product team here in support. To provide this feedback to the correct team, please file a bug.

The issues you are experiencing can be mostly, if not completely, avoided. However, that is only the case if projects are handled properly when setting up a shared project scenario from the get go. The drawback is that you run into plenty of issues if set up steps were not taken regarding collaboration when the projects were created (the "glitches" as you call them), you run into the "duplicated clips" issue.

Premiere Pro has largely solved the problem by creating Team Projects (Beta), which I recommend to you if you continue to collaborate with other editors.

Please read my post: Re: Any way to prevent dupes in Premiere Project file?  for ideas on how to avoid some of the problems.

The key elements are to set up the following your own project before attempting to work with other editors' projects. Do the following:

1. Prior to beginning work on the master project, make sure that you enable 'Write XMP ID to files on import' in Preferences > Media.
2. Disable the "Allow Duplicate Media During Project Import" in the panel menu of the Media Browser.

File a bug for removing any additional clip duplicates that you don't need to be duplicated that might enter the project in progress or from an associate that was not aware how to set up their project properly (with the above two items in mind).

I hope this helps you in future projects.

Thanks,
Kevin

coming from After Effects, it was a consolidate footage command that will erase all the duplicate media in your project panel (as long as it does not have other interpret footage settings). I see premiere only have "remove unused" (under edit).

You should at the very least be able to delete a clip and have an offline representation left in your timeline with a clip name, file path and timecode. If you had to manually find the clips and timecode and re-edit the clips in, at least it would be possible. Trevor_Asq +1, I feel your pain You can right click and 'make offline'

make offline will offline the clip, but it will still be linked to the off line source in your bin. delete that and the clip is gone from your timeline/s. another useful feature from after effects is to replace source from other source. you can alt drag a new source over the old and it will replace it right in the project panel.

these two features, consolidate footage and replace source, apparently don't exist in premiere...

here's a long thread about the duplicated footage issue:

Any way to prevent dupes in Premiere Project file?

+1, I feel your pain

You can right click and 'make offline'