Hi,
I have not been able to reproduce your issue: in JMP 14.1 the line of fit is recalculated and is shown correctly before/after the "Show Excluded" option is selected. Could you share with us the version of JMP you are using? Also, do you have the same problem using one of the example files such as Big Class (e.g. Weight x Height by Sex)? If you still have the problem with the Big Class file, could you share the step by step process you used to create these plots?
If all else fails, you may try to reset your preferences (File > Preferences > Reset to Default), Apply or OK, close JMP and reopen it.
Best,
TS
Thierry R. Sornasse