Ok, I figured out how to delete Layout2. Somehow AutoCAD does not technically recognize this layout until it's manually set active. But another way is to use Lisp to do it which I've now included in the first line in the updated 11x17-2.scr attached.
FYI: Now this updated script as well as the previous one I posted only works on drawings that have a Layout1. Since drawings you've already ran the script on previously renamed Layout1 to 11x17, then the script will no longer have any impact. This updated script needs to be applied on the original converted set of drawings that still have Layout1.
Once again here's the line by line explanation of the updated 11x17-2.scr:

Line1: (foreach x(dictsearch(namedobjdict)"acad_layout")(if(= (car x)3)(setvar"CTAB"(cdr x))))
This is a series of lisp functions that activates all layouts by setting each current including Layout2
Line2: _.TILEMODE 1
This executes Tilemode and sets it to 1 so that the current tab is on Model
Line3: _.-LAYOUT _D Layout1
This executes the command line version of Layout command to Delete Layout1
Line4: _.-LAYOUT _T 11x17.dwt Layout1
This executes the command line version of Layout command again inserting from Template file 11x17.dwt Layout1
Line5: _.-LAYOUT _R Layout1 11x17
This executes the command line version of Layout command again but this time Renames Layout1 to name of 11x17
Line6: _.-LAYOUT _D Layout2
This executes the command line version of Layout command this time to Delete Layout2
Line7: _.CTAB 11x17
This executes Ctab setting the current layout to 11x17
Line8: _.Mspace
This executes Mspace command changing the current space to inside the vport in layout 11x17
Line9: _.-Layer _T 0
This executes the command line version of Layer and then Thaws layer 0
Line10: _S 0
This continues with the Layer command by setting the current layer as 0
Line11: _F *
This continues with the Layer command and Freezes (* = All layers) except the current layer which is set as 0
Line12: _T *titleblock_x
This continues with the Layer command and Thaws layer matching name: *titleblock_x
Line13:
Empty line = Return which completes the Layer command
Line14: _.Zoom _E
This executes Zoom command and then Extents while still inside the vport
Line15: _.-Layer _T *
This executes the command line version of Layer again but this time Thaws all (* = All layers)
Line16: _F level10,level11,level12,level13,level14
This continues with the Layer command and Freezes layers matching names: level10,level11,level12,level13,level14
Line17:
Empty line = Return which completes the Layer command
Line18: _.Pspace
This executes Pspace command to return back to Layout from inside vport
Line19: _.Qsave
This executes the Qsave command
Line20:
Empty line = Return which executes the previous last command
PS:
1. All main commands begin with an underscore "_" and a period "."
The "_" tells AutoCAD to use its native language commands which is English
The "." tells AutoCAD to use the built-in command even if it has been undefined
2. Sub command prompts only need to include "_" because these can't be undefined but do still have the native English language command names.
3. Some main commands when preceded with a hyphen "-" executes without invoking a dialog box allowing the user to respond to the subsequent prompts at the command line