Conditional \bye?

One solution might be to define a custom \bye command, for example \mybye, in the main document. In the subdocument you can perform a check if this command is defined, if not then you define it to be \bye. The definition in the main document can be empty.

Checking if a command exists can be done with \ifcsname (which is an e-TeX macro).

MWE, main document:

Hello from master document\par
\def\mybye{}
\input subdocument
more text in master document
\bye

subdocument:

\ifcsname mybye\endcsname\else\def\mybye{\csname bye\endcsname}\fi
Hello from subdocument\par
\mybye

You can use a macro only defined in the main file.

file dcu.tex

\def\ABCDEFGHIJK{}

\input dcu1

\input dcu2

\bye

File dcu1.tex

This is the first file

\ifx\ABCDEFGHIJK\undefined\csname bye\expandafter\endcsname\fi

File dcu2.tex

This is the second file

\ifx\ABCDEFGHIJK\undefined\csname bye\expandafter\endcsname\fi