Find text (NO whole words only) and Replace

I came across the same problem and accidentally found that I had to clear out the search and replace fields and close the edit PDF window. When I did a new search or search and replace, the Whole Words Only option was unselected.

This may be achieved with javascript though.

Here's a Band-Aid remedy(not elegant, not perfect but useful):

for (var p = 0; p < this.numPages; p++)
{
var numWords = this.getPageNumWords(p);
for (var i=0; i<numWords; i++)
{
var ckWord = this.getPageNthWord(p, i, true);
if ( ckWord == "Acrobat")
{
var q = this.getPageNthWordQuads(p, i);
// Convert quads in default user space to rotated
// User space used by Links.
m = (new Matrix2D).fromRotated(this,p);
mInv = m.invert()
r = mInv.transform(q)
r=r.toString()
r = r.split(",");
l = addLink(p, [r[4], r[5], r[2], r[3]]);
l.borderColor = color.red;
l.borderWidth = 1;
l.setAction("this.getURL('http://www.example.com/')");
}
}
}

Note that the script above creates a red rectangle around the word(s) found. It also converts them to a hyperlink, but you  can modify the script to whatever way you need to behave.

This script example is referenced in the Adobe Acrobat SDK JavaScript API Reference,  "Doc methods",  Example 2, Page 232

This is an action than can be employed as a mouse-up action or as bacth using the Acrobat's built-in Action Wizard tool.

See slides:

You can reuse this action as many times as you need it. To perform a different search each time  just change the string of text inside the quotes in the line shown below:

if ( ckWord == "Acrobat")

It can only replace whole words.