The same issue happens when you define a complete new tool with a shortcut using bl_keymap. On first Add-on activation, the shortcut works. On restarting Blender, it is non-functional. But if you reload all scripts while Blender is still running, the shortcut works again. I have used this class from the Templates to verify this behavior:

bl_info = {
    "name": "Shortcutter",
    "author": "Bug Reporter",
    "version": (1, 0),
    "blender": (2, 80, 0),
}

import bpy
from bpy.types import WorkSpaceTool

class MyTool(WorkSpaceTool):
    bl_space_type='VIEW_3D'
    bl_context_mode='OBJECT'

    # The prefix of the idname should be your add-on name.
    bl_idname = "my_template.my_circle_select"
    bl_label = "My Circle Select"
    bl_description = (
        "This is a tooltip\n"
        "with multiple lines"
    )
    bl_icon = "ops.generic.select_circle"
    bl_widget = None
    bl_keymap = (
        ("view3d.select_circle", {"type": 'LEFTMOUSE', "value": 'PRESS'},
         {"properties": [("wait_for_input", False)]}),
        ("view3d.select_circle", {"type": 'LEFTMOUSE', "value": 'PRESS', "ctrl": True},
         {"properties": [("mode", 'SUB'), ("wait_for_input", False)]}),
    )

    def draw_settings(context, layout, tool):
        props = tool.operator_properties("view3d.select_circle")
        layout.prop(props, "mode")
        layout.prop(props, "radius")


def register():
    bpy.utils.register_tool(MyTool, after={"builtin.scale_cage"}, separator=True, group=True)

def unregister():
    bpy.utils.unregister_tool(MyTool)

if __name__ == "__main__":
    register()

Is this something that's on the ToDo list for 2.81 already? Or is there a workaround for it? Not being able to have modifier keys for custom tools limits the use quite a bit.

when will solve this problem? I can't advance because of it in my development

Hi @Max Derksen (Derksen) , if you are looking for a workaound for the problem of custom tools not working on Blender restart, you will find it in addons/mesh_snap_utilities_line/__init__.py
A simplified version of it is in: https://raw.githubusercontent.com/Shriinivas/blenderbezierutils/master/blenderbezierutils.py
(Essentially, you would need to register the tool and keymap in some roundabout way)

@Shrinivas (Shrinivas) (Shrinivas) , thanks, I'll try this for the instrument. What about saving the shortcuts in the settings addon? that doesn't work either

@Max Derksen (Derksen) Maybe there is also an option for saving the shortcuts in the workaround. Just check keys.py in snap utilities.
I am an add-on developer and faced the same issue in my tool. I got the pointer about this workaround from one of the users (thanks @yoshiki nosaka (sakana3)).

I think this is a high priority subject around keys save and more clear information about this
I tried to modify a key and at the same add another one. I had to change addon_keymaps to user_keymaps = [] but I could not register the other shortcut at the same time so I put user_keymaps in the settings too and I get back and all the default keys in mesh of all maps were erased. I had a save. but doing this because my shortcut was never registred. I see kmi.active=True on old scripts but I never found an explanation. some people use timers other handlers and I saw an update on a property from addon pref. why to go there? well I'm still a noob but it's not possible to improve this to be more easy to use? I think this is a priority as the fact to have new keys in new versions added to own keys config. I don't show the answer of Brecht about this again...I saw a script to find duplicates that's a good begining

I have a key reappearing even when the addon is totally uninstall. I even purge py cache (to see if any effect). It should be a problem in user.pref. but really I don't get it and still reading more infos. I found this https://blenderartists.org/t/key-config-confusion/637985/4 the last comment. it is maybe a little hard, and maybe he didn't understand how it's working. but please provide more clear info about all this. I can disable the key but not erase it. and it's getting back when I uninstall another addon with the same class in. so I changed the name class. no effect.
I found the actual help was in 2.73 and maybe before. this is a good example but plz do more that put 2.8 in the BL at first. I watch several "multi" addons and they are all reporting some issues about this. so with my little beginner level it's just a pita

I think problem hidden here

\blender-2.82-e5b788bad8bc-windows64\2.82\scripts\modules\bpy\utils\__init__.py

# Convert the class into a ToolDef.
def tool_from_class(tool_cls):
    # Convert class to tuple, store in the class for removal.
    tool_def = ToolDef.from_dict({
        "idname": tool_cls.bl_idname,
        "label": tool_cls.bl_label,
        "description": getattr(tool_cls, "bl_description", tool_cls.__doc__),
        "icon": getattr(tool_cls, "bl_icon", None),
        "cursor": getattr(tool_cls, "bl_cursor", None),
        "widget": getattr(tool_cls, "bl_widget", None),
        "keymap": getattr(tool_cls, "bl_keymap", None),
        "data_block": getattr(tool_cls, "bl_data_block", None),
        "operator": getattr(tool_cls, "bl_operator", None),
        "draw_settings": getattr(tool_cls, "draw_settings", None),
        "draw_cursor": getattr(tool_cls, "draw_cursor", None),
    })
    tool_cls._bl_tool = tool_def

    keymap_data = tool_def.keymap
    if keymap_data is not None:
        if context_mode is None:
            context_descr = "All"
        else:
            context_descr = context_mode.replace("_", " ").title()
        from bpy import context
        wm = context.window_manager
        kc = wm.keyconfigs.default  #  <-------------------------<-----------------------< HERE
        if callable(keymap_data[0]):
            cls._km_action_simple(kc, context_descr, tool_def.label, keymap_data)
    return tool_def

I've tested it with kc = wm.keyconfigs.user, everything work's well.
API: keyconfigs.default
API: keyconfigs.user

If it's so, then one line in function unregister_tool (scripts\modules\bpy\utils\__init__.py) should be changed same way from

kc = wm.keyconfigs.default

to

kc = wm.keyconfigs.user

otherwise addon will throw error when you deactivate it

@Cirno (Cirno)
All good for now, thanks for quick workaround

Tested the fix provided by @Cirno (Cirno) and can confirm this works! Attatching a diff for merging in case one of the devs wants to use it.

I want to bump this, since fix seems to be really so simple (one line of code). @Campbell Barton (campbellbarton)