Anytime you click on a Bid/Alternate/Change Order name in the Bid/Section grid, or check the box for "Select all Bid sections", you are viewing and updating the cumulative Markups for the entire Bid (and Accepted Alternates if that box is check also). Changes made on the Markups Details will overwrite individual 'per-Section' Markups. This cannot be undone.
If you adjust Labor Burden (Labor Burden Override) while in "All Sections" view, you are wiping out the unique Labor Burdens for every Wage Type and replacing them with a single value, allocated to whatever Labor Cost Code you have setup as your "Labor Burden Override". See Related Articles for more information.
As a reminder, selecting "All Bid Sections", and then opening up the Indirect Expenses window wipes out all previously-configured Indirect Expenses. If you use this "Override" function, you must reconfigure all Indirect Expenses during the same session, see Related Articles for more information.