I'm using the 3.1.1 Krita AppImage on Linux and upgraded from Krita 3.0. I made great use of the circle pop-up menu in the previous version, as soon as I started using 3.1.1 though, pretty much every brush I had in the pop-up menu has been removed. There's nothing in the pixel-art pallet, ink pallet, block, circle, erasers, FX, mix, and a bunch of others.

Is there anything I can do to get it back easily? Thanks.

The xml file in which the tags are configured use filenames + md5 hash to identify the presets.

Maybe the md5 hash of the presets have changed in the 3.1

You can try to copy the 3.0 paintoppresets over the 3.1 paintoppresets or you can manually add the current presets to the tags

You can also create your own tags and organize it the way you want.

If you really want to avoid loosing the tags updating, you can keep a set of presets on the resources folder and assign them to tags
The presets on the resources folder are never touched, unless you deliberately override or delete a preset.

Timothee has removed the old tags and created some new tags. Unfortunately, the tags are also saved locally, so they cannot be removed. You can either remove all the tags that are assigned to the dummy resource in your local tags xml file.

Could anyone walk me through how I should do this? I'm on Ubuntu 16.04. I'm afraid I'm just not entirely sure what to do here or how I go about getting all of my pop menus working on 3.1. I don't know what tags are, or where the XML file is or how I should be altering it. If it helps at all, nothing was customized at all. They were just the standard sets of brushes.

Go to the brush selector docker. Select "all". Select a brush, right-click and assign it one of the tags. Selecting that tag in the right-click popup will show that brush.

This worked, obviously, but I'm pretty unhappy about having to redo all of the brush menus myself. I hope this isn't a persistent thing with every update.

No, well, maybe. We're rather struggling with how to make it possible to distinguish between system tags, making it possible to delete system tags, and making it possible for us to replace system tags. But your own tags shouldn't have changed, and if you'd used the system tags to tag other brushes, those should still be tagged, even after updating.

But we need to replace that whole kludge with a proper solution, probably a real database stored in sqlite.

For those who, like me, arrived to this thread looking for help on this bug:
Custom tags keep disappearing sometimes (not clear under which circumstances) still in v3.1.1. The bug is not yet fixed. Obviously the devs are working hard for a solution, we've to trust them.

Meanwhile, I have proposed a workaround in another thread in this forum:
Tags Lost - WORKAROUND https://forum.kde.org/viewtopic.php?f=139&t=137749#p370930

That has allowed me to work smoothly with all my custom tags, without disrupting my workflow, while I look forward to a final, robust solution for this very serious bug.