If data doesn't exist add to bottom of list - arrays

Question

Basically I'm working on a excel document which copies values from this workbook into another if they match. So if they have the same ID and a "yes" then a field is updated. However in some instances it may be that the ID doesn't exist in the workbook im copying to, but if there is a "yes" I would like to add it to the next empty row.
Below is what I have so far
Dim fpath As String
Dim owb As Workbook
Dim thisone As String
Dim Siteref(1000) As String, siteref2(1000) As String, sitename(1000) As String, sitename2(1000) As String
fpath = "my file path"
Set owb = Application.Workbooks.Open(fpath) 'open location and file
Dim Master As Worksheet 'declare both
Dim Slave As Worksheet
Set Slave = owb.Worksheets("Schedule") 'sheet in workbook im copying too
Set Master = ThisWorkbook.Worksheets("Tbl_Primary") 'sheet from workbook im in
For i = 1 To 1000 '(the slave sheet) 'for first 1000 cells
For j = 1 To 1000 '(the master sheet)
If Master.Cells(j, 2).Value = "" Then
GoTo lastline
End If ' if ID cell is blank jump to last line
If Master.Cells(j, 2).Value = Slave.Cells(i, 1).Value And Master.Cells(j, 65).Value = "Yes" Then
Slave.Cells(i, 4).Value = Master.Cells(j, 18).Value 'If the ID equals that in the slave sheet and there is a yes ticked the copy address
End If
lastline:
Next
Next
MsgBox ("Data Transfer Successful")
Application.DisplayAlerts = False
ThisWorkbook.Worksheets("Tbl_Primary").Delete 'delete sheet
Application.DisplayAlerts = True
ThisWorkbook.Save
ThisWorkbook.Close 'save and close it

Answer 1

Give this one a try and let me know if it works. I wrote it "blind" without testing. So, I am not entirely sure it will work:
Dim bolFound As Boolean
Dim lngLastRow As Long
Dim fpath As String
Dim owb As Workbook
Dim Master As Worksheet 'declare both
Dim Slave As Worksheet
fpath = ActiveWorkbook.Path
Set owb = Application.Workbooks.Open(fpath) 'open location and file
Set Master = ThisWorkbook.Worksheets("Tbl_Primary") 'sheet from workbook im in
Set Slave = owb.Worksheets("Schedule") 'sheet in workbook im copying too
'
lngLastRow = Slave.Cells.Find("*", searchorder:=xlByRows, searchdirection:=xlPrevious).Row
For j = 1 To 1000 '(the master sheet)
bolFound = False
For i = 1 To 1000 '(the slave sheet) 'for first 1000 cells
If Trim(Master.Cells(j, 2).Value2) = vbNullString Then Exit For 'if ID cell is blank jump to last line
If Master.Cells(j, 2).Value = Slave.Cells(i, 1).Value And _
Master.Cells(j, 65).Value = "Yes" Then
Slave.Cells(i, 4).Value = Master.Cells(j, 18).Value 'If the ID equals that in the slave sheet and there is a yes ticked the copy address
bolFound = True
End If
Next
If bolFound = False And _
Master.Cells(j, 65).Value = "Yes" Then
Slave.Cells(lngLastRow, 4).Value = Master.Cells(j, 18).Value 'adding the new entry to the list
lngLastRow = lngLastRow + 1
End If
Next
MsgBox ("Data Transfer Successful")
Application.DisplayAlerts = False
ThisWorkbook.Worksheets("Tbl_Primary").Delete 'delete sheet
Application.DisplayAlerts = True
ThisWorkbook.Save
ThisWorkbook.Close 'save and close it

Answer 2

NOT tested.
Dim fpath As String
Dim owb As Workbook
Dim thisone As String
Dim Siteref(1000) As String, siteref2(1000) As String, sitename(1000) As String, sitename2(1000) As String
Dim lastRow As Long
fpath = "my file path"
Set owb = Application.Workbooks.Open(fpath) 'open location and file
Dim Master As Worksheet 'declare both
Dim Slave As Worksheet
Set Slave = owb.Worksheets("Schedule") 'sheet in workbook im copying to
Set Master = ThisWorkbook.Worksheets("Tbl_Primary") 'sheet from workbook im in
For i = 1 To 1000 '(the slave sheet) 'for first 1000 cells
For j = 1 To 1000 '(the master sheet)
If Master.Cells(j, 2).Value = "" Then
Exit For
End If ' if ID cell is blank jump to last line
If Master.Cells(j, 2).Value = Slave.Cells(i, 1).Value And Master.Cells(j, 65).Value = "Yes" Then
'If the ID equals that in the slave sheet and there is a yes ticked the copy address
Slave.Cells(i, 4).Value = Master.Cells(j, 18).Value
End If
If Master.Cells(j, 65).Value = "Yes" Then
lastRow = Slave.Cells(ActiveSheet.Rows.Count, "D").End(xlUp).Row
'if yes found, copy value
Slave.Cells(lastRow + 1, 4).Value = Master.Cells(j, 18).Value
End If
Next
Next
MsgBox ("Data Transfer Successful")
Application.DisplayAlerts = False
ThisWorkbook.Worksheets("Tbl_Primary").Delete 'delete sheet
Application.DisplayAlerts = True
ThisWorkbook.Save
ThisWorkbook.Close 'save and close it