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I'm trying to panelize two different layouts.

I'm trying to panelize two different layouts. The tool numbers in the drill files are not the same for the same drills. When the drill layers are synchronized, I get a new drill file with some of the hole sizes wrong, i.e. if the .046 drill is tool 01 in the first file and tool 02 in the second file, the software cannot handle it. Seems pretty basic... Help!
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Thanks for submitting a support ticket and including a sample file.  Layer synchronize, panelize, and all other commands do not modify/change the drill tool number (unless you choose to by using command Edit | Properties..., and change the Tool number). 

During import FAB 3000 will automatically transcode the Drill tool numbers into one master Drill table.  The is the same for your Gerber files where the "Dcode number" will also be transcoded into a master aperture table.  This transcoding allows FAB 3000 to normalize the data and easily merge multiple boards.

Note:  For example if board one has 5 Drill sizes, Tools 1-5 are defined in the FAB 3000 master drill table.  If I load another board with 5 different drill sizes, Tools 6-10 are defined in the master drill table (even though in the second drill file it shows tools 1-5 they get transcoded into the next available tool numbers in the FAB 3000 master drill table).  See quick tutorial:

Please let me know if I answered your question, and thanks again for submitting a support ticket.
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