If you need to edit the capture and bring it back in I’m not seeing the workflow.
Captured image on phone → Devonthinks
Image needs cropping & adjustment and want to send it to → Affinity Photo
then save it and have it back in DT
I basically had to export it, edit it, save to a file location, make a new import, delete the original and that seems a looong way around the elbow to get where I’m trying to go.
Probably a forest for trees issue, thought I’d ask as I’m just not seeing it.
First, welcome to the forum. Second where exactly are you “trying to go”? 
Why import the undedited image into DEVONthink in the first place if what you want in DEVONthink is the edited version and not the original?
On the assumption you’re editing in Affinity Photo why don’t you simply do that first and then import into DEVONthink the edited image?
I’m sure I’m missing something (and sorry if I am) but I really don’t understand why your first step (importing the unedited image into DEVONthink) is there.
Stephen
If you think of it in workflow terms then if I can scan everything, add metadata in a sitdown, then return to it later to adjust/crop/edit/whatever then everything is housed and set and just needs refining.
For instance my old Lightroom workflow was card import and meta-data-entry creation then if I needed to edit in PS I could edit and when I saved it updated the file in LR. There wasn’t a need to export the photo then re-import it and re-add meta to it. It was picked up in the housed directory, edited in the housed location, and updated when it was done.
If I do a bulk scan into a folder, then I have to move an editing session to the forefront which is always a lot longer task and not at all data-entry like. So in the GTD kind of mindset it’s crossing two very different lists together that have very different requirements for accomplishing.
Just seems like their could be an Edit → Choose your app → it loads from the directory → you edit & save → the file modified time is updated → devon refreshes the image/pdf/whatever because the modification time has been updated.
Why is “Open with” not working for you?
There is already a Data > Open With option in DEVONthink. However, Affinity Photo works with its own format when making adjustments. That requires an export of the altered file after your edits. That is a new file. It is not the file in DEVONthink. So it won’t update the file in DEVONthink as it’s not the same file, regardless of the name.
Dang. I was looking in two places. On the image itself right click does not haven an Open with or Edit with. Its edit dialog was confusing me. Then on the top bar I wasn’t looking at Data I was looking under Edit and also didn’t grok the Data/Open with.
As to Affinity if you make the project layered it will create an afp file. If you only do adjustments/resize/crop/etc or if you do layers and then flatten it back down it will save it in the original file format.
And as a summary Devon will update (tested & validated.)
So I apologize for not seeing the workflow under the headings and methods required to get it accomplished. It looks like it existed all along and I was just blind.
Thank you all for your corrections and insight!
Good to know.
I’m an old Adobe diehard. Affinity products just don’t get traction with me (with no offense to them).
You’re welcome and we’re glad to have you here. 
I used to be an adobe certified trainer all the way back to 3.0 hah. I loved Adobe but their model, updates, bloatware and more finally caused me to sever my relationship. The things they add aren’t things I need and the cost of actually owning something vs renting it is always nice. There is a lot of parity between the products with only a few places it falls off the rails and even those have gotten more narrow over time. The last thing I had to migrate was my LR “classic” (love that…) catalogs to Exposure & Capture One.
It’s hard to break away from things you’re used to but I’m here because Evernote became something I wasn’t. Gotta stay flexible to the changing landscape of what we use, even if it causes me to stickynote a few keyboard shortcuts I don’t quite have muscle memory down for. 
Thanks again for your help!
Glad to be of service