Looks like your setup (and intentions) are the same as mine.
Firstly, the channel numbers that appear when you are mapped to a bocquet which have channel numbers less than 101 started appearing a couple of months ago (around the same time the "detach from bocquet" feature was added). With those, simply disable them rather than deleting them. It's the first checkbox in your screenshot. You can multi-select a load of them, click on the "Edit" button then ensure the "Enabled" checkbox is unchecked - you also need to CHECK the box immediately to the right of it to enable the "multi-select" feature to update all the channels you selected.
Delete will not work (putting aside the "detach from bocquet" feature which should stop this happening) - if a channel is in a bocquet, it will be re-added when the bocquet is refreshed (i.e. at boot time and periodically). Disabling them keeps them part of the bocquet but invisible from your clients. To also hide them from the web ui, drop the menu down next to the "Enabled" button and set the filter to "Yes" - this will hide any disabled channels from the web ui (you'll need to do this on every browser you use or if you clear your cookies).
Next, you seem to have a load of duplicate "genuine" Sky channels in that list (i.e. multiple ITV versions assigned to channel 103) which suggests some channels are manually added (unintentionally) or the bocquet is a bit screwed.
* In your bocquets list, have you got both "Enabled" and "Automap" checked only for bocquet 5?
* Does the "# Services" column and "# Services Seen" numbers match in the bocquets list? I'm seeing 640 channels in that bocquet at the time of posting
* What happens if you uncheck both boxes for bocquet 5 in the bocquets list - are any channels left over once TVHeadend removes the ones in bocquet 5?