How to avoid destroying data when using tkinter Toplevel parent/child windows?

The code you have can be changed fairly easily to fix the problem. Tkinter supports something called "Variable Classes" — see The Variable Classes (BooleanVar, DoubleVar, IntVar, StringVar) — which are very handy for storing and passing around data within tkinter apps. In particular, Entry widgets support storing their contents in one (see Entry widget options) simply by passing one to it via the textvariable= keyword argument when its created. Once that's done, the widgets current (or last) value can be retrieved at any time whether the Entry still exists or not.

Below is a modified version of your code with the modifications needed to create and use one to pass information that's put into the widget in the child window back to its parent. I've indicated the most important changes with # ALL CAPS COMMENTS. Also note that I have also reformatted your code so it follows the PEP 8 - Style Guide for Python Code recommendations and is more readable. I strongly suggest you read and follow these guidelines.

import tkinter as tk

class Parent(tk.Tk):
    def __init__(self):
        tk.Tk.__init__(self)

        self.dic = {}
        self.dic['var'] = ['default']
        self.dic['child1_value'] = tk.StringVar(value='')  # ADDED.

        self.title("Parent")
        self.button1 = tk.Button(self, text="open Child1",
                                 command=self.open_child1, width=20)
        self.button1.grid(row=0, column=0, padx=5, pady=5)
        self.button2 = tk.Button(self, text="Get Child1 config",
                                 command=self.get_child1_value, width=20)
        self.button2.grid(row=0, column=1, padx=5, pady=5)
        self.label1 = tk.Label(self, text="", width=10)
        self.label1.grid(row=0, column=2, sticky='ew')

        self.Child1_from_parent = Child1(self)
        self.Child1_from_parent.withdraw()

    def open_child1(self):
        self.Child1_from_parent.deiconify()

    def get_child1_value(self):
        self.label1.config(text=self.dic['var'][0] + '\n' +
                                self.dic['child1_value'].get())  # CHANGED.


class Child1(tk.Toplevel):
    def __init__(self, master):
        tk.Toplevel.__init__(self, master)
        self.frame  = tk.Frame(self)

        self.title("Child")
        self.label1 = tk.Label(self, text="Config 1", width=10)
        self.label1.grid(row=0, column=0)
        # ADDED `textvariable=` keyword argument.
        self.child1_entry = tk.Entry(self, width=10,
                                     textvariable=master.dic['child1_value'])
        self.child1_entry.grid(row=0, column=1, padx=5, pady=5)
        self.child1_entry.insert(tk.END, self.master.dic['var'][0])
        self.child1_entry.bind('<Return>', self.update_value)
        self.button4=tk.Button(self, text="Close", command=self.close_child1, width=20)
        self.button4.grid(row=0, column=2, padx=5, pady=5)
        self.button5=tk.Button(self, text="destroy", command=self.destroy_child1,
                               width=20)
        self.button5.grid(row=0, column=3, padx=5, pady=5)

    def update_value(self, event):
        self.master.dic['var'][0] = self.master.Child1_from_parent.child1_entry.get()

    def close_child1(self):
        self.withdraw()

    def destroy_child1(self):
        self.destroy()


def main():
    Parent().mainloop()

if __name__ == '__main__':
    main()

If I understand your question correctly then this code may help.

It is a minimal demonstration of a one parent many children implementation.

All data and micro changes to each child are maintained after closing child.

Keyboard short-cuts give access to all children and parent

Parent is accessible while child is active.

Real exit is via gate keeper dialog from messagebox.

Creating children is easy and open ended.

import tkinter as tk
from tkinter.messagebox import askyesno

def flexx(m, r = 0, c = 0, rw = 1, cw = 1):
    if r !=  None:
        m.rowconfigure(r, weight = rw)
    if c !=  None:
        m.columnconfigure(c, weight = cw)

class child(tk.Toplevel):

    def __init__(self, master, title, key):
        super().__init__(master)
        self.transient(master)
        self.title(title)
        flexx(self)
        self.protocol('WM_DELETE_WINDOW', self.toggle)
        self.bind('<Escape>', self.toggle)
        self.bind(key, self.toggle)

    def toggle(self, event = None):
        '''toggle child on|off'''
        if self.winfo_viewable():
            self.withdraw()
        else:
            self.deiconify()
            self.focus_force()


class parent(tk.Tk):

    def __init__(self, title, icon = None):

        super().__init__()
        self.title(title)
        flexx(self)
        self.protocol('WM_DELETE_WINDOW', self.closer)
        self.bind('<Escape>', self.closer)
        if icon:
            self.iconbitmap(default = icon)
        self.withdraw()

    def maker(self, title, key, geom):
        anon = child(self, title, key)
        # Connect parent and child
        self.bind(key, anon.toggle)
        anon.geometry(geom)
        return anon

    def closer(self, event = None):
        if askyesno(
            title = 'Confirm', message = 'Really',
            detail = 'Close Program?', default = 'no'):

            self.destroy()

if __name__ == '__main__':

    the = parent('The Parent', icon = None) # icon = '.\\Icons\\Py-006.ico')
    w,h,x,y = 500, 500, 100, 50
    the.geometry(f'{w}x{h}+{x}+{y}')
    the.boy = the.maker('harri', '<Control-h>', f'200x200+{x+w+5}+{y}')
    the.girl = the.maker('suzie', '<Control-s>', f'200x200+{x+w+5}+{y+235}')
    # make all other children
    # inter-connect all children
    the.girl.bind('<Control-h>', the.boy.toggle)
    the.boy.bind('<Control-s>', the.girl.toggle)
    the.deiconify()
    the.mainloop( )