Remove subsection header in the document, keep it in the TOC

Don't use subsection{Header1} but instead use

refstepcounter{subsection}
addcontentsline{toc}{subsection}
  {%
    ifnum2>value{secnumdepth}elseprotectnumberline{thesubsection}fi Header1%
  }

Complete MWE:

documentclass[]{article}

begin{document}
tableofcontents

section{something}
refstepcounter{subsection}
addcontentsline{toc}{subsection}
  {%
    ifnum2>value{secnumdepth}elseprotectnumberline{thesubsection}fi Header1%
  }
end{document}

Result:

One could as well create a macro that does take two arguments, the sectioning level and the heading and create a TOC entry without typesetting a heading, if this is needed multiple times. The following should work for the standard classes.

usepackage{pdftexcmds}
makeatletter
def@getsecnum@fin#1else#2fi{fi#1}
def@getsecnum@nonefi{fi1000}
newcommand*@getsecnum@a[2]
  {%
    fiifnumpdf@strcmp{#1}{#2}=0 @getsecnum@fin
  }
newcommand*@getsecnum[1]
  {%
    ifnumpdf@strcmp{#1}{part}=0 @getsecnum@fin{-1}%
    else@getsecnum@a{#1}{chapter}{0}%
    else@getsecnum@a{#1}{section}{1}%
    else@getsecnum@a{#1}{subsection}{2}%
    else@getsecnum@a{#1}{subsubsection}{3}%
    else@getsecnum@a{#1}{paragraph}{4}%
    else@getsecnum@a{#1}{subparagraph}{5}%
    else@getsecnum@none
    fi
  }
newcommandTOConlySection@[3]
  {%
    ifnum#1>c@secnumdepth
    else
      refstepcounter{#2}%
    fi
    addcontentsline{toc}{#2}
      {%
        ifnum#1>c@secnumdepth
        else
          ifnum#1=-1
            theparthspace{1em}%
          else
            protectnumberline{csname the#2endcsname}%
          fi
        fi
        #3%
      }%
  }
newcommandTOConlySection[2]
  {%
    expandafterTOConlySection@expandafter
      {romannumeral-`0@getsecnum{#1}}{#1}{#2}%
  }

Usage would be

TOConlySection{part}{part heading}
TOConlySection{section}{section heading}
TOConlySection{subsection}{subsection heading}

If this is needed for the included pdf, then you can use option addtotoc={⟨page number ⟩,⟨section ⟩,⟨level ⟩,⟨heading ⟩,⟨label ⟩} for includepdf.

addtotoc={1,subsection,2,<heading>,<label>}

Example:

documentclass{article}
usepackage{pdfpages}
begin{document}
tableofcontents
section{A section}
See subsection~ref{subsec:H1} on page pageref{subsec:H1}.
includepdf[pages=-,addtotoc={1,subsection,2,Header1,subsec:H1}]{dummy}
end{document}

Result: