This may be caused by at least two factors (maybe both of them):
1. Your sheet is displaying three decimal zeroes, but value of cell is
another. Check Format → Cells (or RMB → Format Cells) if they are formatted to
have three decimal zeroes.
2. Displayed zero is effect of computation of formula entered into cell. By
default, LO searches only formulas. To change this, in find and replace window
you have to click "more options" button and change "search in" to "values".
In both cases, you can check value of selected cell in formula field (right
above the sheet).
While you are in "More options", ensure that "current selection only" is
checked. Otherwise, you may unintentionally destroy your other data. Perhaps
creating backup copy of file before search-and-replace is good idea.
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