The "size" issue is because the equation editor is not able to keep
styles separately for each equation, the way that MathType can. You
may be successful when inserting equations, to have them set to
several different font & size styles, but as you discovered, when you
save and reopen the document, it's not as you left it.

Copying a large Word document and pasting it into another is probably
not ever a good idea, even if the new document starts out as a blank
document. If you absolutely have to keep it as one document, there are
a few things you can do to reduce the file size, but you should give
primary consideration to making several smaller documents in place of
the large one. You've seen one problem that can arise with the
equations, but as a rule we don't recommend copying an equation from
one document and pasting into another (or even within the same one).
Actually that'll work out all right some of the time, and perhaps even
most of the time, but at some point Word will lose some of the OLE
information in the equation object (that's the information that tells
it the object came from Equation Editor). If that happens, you'll
probably not know it right away; you'll only discover it when you try
to edit the equation, but Word thinks it's a picture, and won't open
it up in Equation Editor. The way to prevent this is to copy the
equation, open Equation Editor as if you were going to create a new
equation, then paste the equation inside the equation editing space
and close Equation Editor.

None of these are perfect solutions, but keeping the document size
"small" to begin with is the closest you'll come to a perfect
solution. The definition of "small" all depends on how many objects
are in the document -- equations, pictures, charts, etc. -- and how
it's formatted.

--
Bob Mathews
Director of Training
Design Science, Inc.
bobm at dessci.com
http://www.dessci.com/free.asp?free=news
FREE fully-functional 30-day evaluation of MathType
MathType, MathFlow, MathPlayer, MathDaisy, Equation Editor

On 28-Feb-2010, ion wrote:

In Microsoft Word 2003, when I add a new inline equation into
a large word document (50+ pages with tables, equations),
the equation vertically aligns with text around it well, i.e.,
bottom aligned.

Overtime, this document grows so huge, that I'd like to either
copy paste the entire document into a new document, or
save it as a new document, to shrink the file size, and
prevent frequent crash of word. But either way, in the new
document that I created, or saved as, all equation now shows
up slightly smaller than it is in the original document, and it
sits slightly higher than the text around it (when looking
at the bottom of the equation and the text).

If I double click the equation, going into edit mode, but don't
make any change and go back to word immediately, then
the equation displays normal again, i.e., the equation font
now looks normal (same as it was in the original document),
and vertically align well with text around it.