A problem could occur if you still have the vacuum line hooked to the EGR valve causing it to open and close. The EGR Valve Position (EVP) sensor will tell the computer that it's opening and the computer will think that exhaust gases are being added to the intake charge and adjust accordingly. Disconnecting the vacuum hose will keep that from happening. You'll still get a code for the EGR valve not opening, but it won't turn your check engine light on, although it may cause it to flash periodically. You shouldn't, however, disconnect the EVP sensor. Doing that will cause it to be stuck in open loop.
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