class svjour3 Package mathptmx Warning: There are no bold math fonts on input line nn

First of all you should not load amsmath, amsfonts and mathptmx before \documentclass. You also don't need fix-cm, since you're using a different font set than Computer Modern.

The issue is simply that mathptmx does not provide bold math fonts, whereas svjour3 applies \boldmath to its sectional titles.

Use a font set based on Times that has bold math fonts.

\documentclass[smallextended,final]{svjour3} % onecolumn (second format)
%
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}

\usepackage{newtxtext,newtxmath}

\usepackage{graphicx}
\usepackage[]{units}
\usepackage{enumitem}
\usepackage{booktabs}
\usepackage[toc,page]{appendix}
\usepackage{url}
\usepackage{hyperref}

\journalname{Found Phys}

\smartqed  % flush right qed marks, e.g. at end of proof