I just ran into this issue for the second time in Affinity Designer. I think it happened when I pressed the Tab key to move between the fields of the Transform panel, but the cursor wasn't in one of the fields, so the Tab key instead hid all the toolbars and panels. I pressed Tab again to bring them back, but a few moments later I noticed the toolbar was missing even though it was checked in the View menu. Selecting and unselecting it or pressing Command-Option-T did nothing to bring it back.
I reset all my preferences last time this happened, but I didn't want to do that again, so instead I opened the ~/Library/Preferences/com.seriflabs.affiniitydesigner.plist file, and the same file from yesterday's backup, and ran a diff. Through trial and error, I found that if I copied the contents of the ToolbarPanelLayout key from the backup, then opened Affinity Designer, the toolbar was back.
Chris B mentioned a fix in Affinity Designer -- is that the same bug I'm describing here? I was running version 1.8.1 when the toolbar disappeared, and updating to 1.8.3 didn't bring it back, but maybe now that I'm on 1.8.3 it won't disappear again.
If this is not the same bug, then hopefully my description helps address this additional problem.