(This discussions assumes managed code and contenttypes attached to the form library)
I've had a lot of problems with columns being updated --also problems with column mappings (This can get crucial when you have workflows dependent on the name staying the same. To get them to work I've had to take some drastic measure. For my infopath projects I first a feature with site columns (I use a named group to be able to locate the columns quickly) and install it on the server. Next in design mode I save my form as source files. Next I exit infopath and go into my source files directory and edit the xsf file. I find where my columns are. Get the guid and find where it's mapped and substitute my guids from my site columns.
Next I reconstitute and InfoPath Form by double-clicking on the xsf and save it to another name. Then I publish it. I've been working with alot of managed code lately so I use a batch file of stsadm commands. When this is done, I know my columns map to my site columns.
Slightly more of a problem to add new columns.
I save all my InfoPath forms to a temporary directory and delete them from the library. Since I'm using a directory with contenttypes, I delete the contenttype from form library where it's attached.
(The forms have to be gone to delete the contenttype from the library. Next I delete the ContentType.)
Then I redeploy my site feature.
I deactive and activate the Site Collections Feature for my site columns. You should be able to see your added columns under Site Columns and the group you used at this point.
Also the Contenttype (assuming your using managed code) should be back. You can check it at Site Settings=>Galleries =>ContentTypes
Next I reattach the contenttype to my form library and reimport my documents.
Let me know if this helps--It not fun
Here's a script for publishing
prompt $D $T$_$P$G
cd "C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\bin"
stsadm -o deactivateformtemplate -url http://portal/sites/ds -filename "C:\Documents and Settings\onisicks\Desktop\INFOPATH FORMS\MDA Announcements\Published\MDAAnnouncements.xsn"
stsadm -o execadmsvcjobs
stsadm -o removeformtemplate -filename "C:\Documents and Settings\onisicks\Desktop\INFOPATH FORMS\MDA Announcements\Published\MDAAnnouncements.xsn"
stsadm -o execadmsvcjobs
stsadm -o retractsolution -name form-mdaannouncements.wsp -immediate
stsadm -o execadmsvcjobs
stsadm -o deletesolution -name form-mdaannouncements.wsp
stsadm -o execadmsvcjobs
stsadm -o verifyformtemplate -filename "C:\Documents and Settings\onisicks\Desktop\INFOPATH FORMS\MDA Announcements\Published\MDAAnnouncements.xsn"
stsadm -o execadmsvcjobs
stsadm -o uploadformtemplate -filename "C:\Documents and Settings\onisicks\Desktop\INFOPATH FORMS\MDA Announcements\Published\MDAAnnouncements.xsn"
stsadm -o execadmsvcjobs
stsadm -o activateformtemplate -url http://portal/sites/ds -filename "C:\Documents and Settings\onisicks\Desktop\INFOPATH FORMS\MDA Announcements\Published\MDAAnnouncements.xsn"
stsadm -o execadmsvcjobs
pause
obviously you will have a different site and different Document. I use WSPBuilder for Site Features. It helps if you pray.
Hope this helps