The table links weren't really destroyed, it's just that in a front end database, the user must have permission to use both the link in the front end and the table in the back end.
The links have their own set of permissions, which you can set separately from the back end permissions. However, I don't think that's going to help much in this case.
The real solution, I believe, is to not let the users see the Database Window, not let them get into Design View, not let them open the Immediate Window (Debug Window in Access 97), etc.
First, you'll need to build a switchboard form. The switchboard, which can be built with the Switchboard Manager or custom built, has command buttons that let the users open their forms and reports. These will be the only way they can interact with the front end application, so you'll maintain control over what they can do.
Then, optionally but just to be safe, modify your forms' and reports' Record Source properties, and list and combo box Row Source properties, to use only Owner Access queries. Owner Access is a setting in query properties (Run Permissions = Owner's) that specifies that the tables are accessed using the query owner's permissions, rather than the user's. The users will then not need any permissions of their own, so you can remove them.
If you have SQL statements in VBA code, you'll also have to make them Owner Access queries, by adding the WITH OWNERACCESS OPTION clause.
Next, you'll need to create a custom menu bar, toolbars, and shortcut menus that remove the Design View and other inappropriate commands. You'll need at least a custom main menu bar, and a custom shortcut menu bar. Using the Toolbars|Customize command, you can build these toolbars and menu bars by dragging the built-in commands you need to your new command bar. (If you need to modify a command's properties, hold down Shift to get a copy as you drag, because otherwise your changes will also apply to the built-in menu items and buttons.) The custom shortcut menu should be specified in the Shortcut Menu Bar property of each form. You may want a separate one for reports as well.
Once you've done all this and tested all the forms and queries, you're ready to cut off access to the design mode facilities. You do this in the Tools|Startup dialog. Specify your switchboard as the Display Form, your customized main menu as the Menu Bar, and clear the check box for Display Database Window. Leave the other options alone for now.
Now close the database and open it again; your startup form should be displayed, and you can test the application the way the user would see it, with only appropriate menus and toolbars. Look for anything that might let them escape into design mode. Especially, right click everywhere to check the shortcut menus. (Because they're context dependent and normally hidden, it's easy to overlook them.) If you find something you need to fix, you can hit F11 to get to the Database Window, and hit Ctrl-F11 to toggle the main menu back to the Access standard one.
Once you think you've got all the design mode facilities locked away, go back into the Startup dialog and clear the remaining check boxes. From then on, when you open the database normally, there shouldn't be any way to get to the tables or queries directly, nor to bring up any design facilities. Do final testing to verify this. At this point, if you find something to fix, you have to close the database and reopen it while holding down Shift, which causes the Startup properties to be ignored.
When you're ready to distribute or implement, log on to Access as the user you want to be the owner, make a copy of the database, and set its AllowBypassKey property to False (see the Help topic). Only the copy you distribute to the users should have this property setting. The original database will be your design copy. From then on, any changes you need to make will be made in your design copy, and you'll build a new copy of the front end for distribution each time. If necessary, use the Tools|Security menu to change the owner of all the database objects.
This sounds like a lot of work, but it's really not that bad, and can be accomplished in a couple of hours--less after you've done it a time or two. Rick Sprague