Hi @Dorothy, glad to see you have worked most of this out already. You clearly sound a lot more clued up than I was when I was new to DevonThink!
You already know these things but, as they weren’t explicitly addressed in the other answers, I thought I’d cover a couple of basic points in case you don’t or are unclear about them.
As you may already know, DT has 2 ways of keeping track of your files; either importing copies of those files into the database, or by indexing files, so they stay where they are in your usual file system but DT maintains a link to that file location. From what you’ve described you have imported your proweave files, as the folders ‘under the hood’ of DT are usually named with letters (but you don’t see that if you just interact with the file through the main DT interface). If you move the file from this folder within Finder it will cause a problem for DT (see below).
You also mentioned:
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My reason for using DT for this purpose is partly because I like things all in one place but also it gives me the chance to annotate the file which is easier in DT than on Pro-weave.
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What has me confused here is how you are able to annotate these files using DT if they are not a compatible file type, or do you mean that you use the DT Info dialogue box to type some information as notes about what’s in these files, rather than editing/annotating the file contents directly?
If it’s the latter then note that you can still do this even if you Index the the files into your DT database rather than physically importing the file. That way you can still have all your proweave files in one place (and just index the folder they’re in), do your annotations as before, and still see the ‘normal’ folder in your file system to open the files directly within proweave etc without any confusion. However there are some limitations of Indexing files you need to be aware of:
First, DT can only keep track of each indexed file provided that you do not change its location or name from within Finder or other applications like proweave. If you break this link however you can fix that by showing DT where the missing file is.
Second, that means that if you index the parent folder of these files DT won’t automatically see any new files you add to it; you will either need to tell DT to update the indexed folder or manually index each proweave file after it is created.
Sorry for the long answer (or I you already knew this) but hopefully that helps fill in any missing gaps in the basics