It introduces additional delay. So the time alignment procedure needs to be repeated.
Can you expand on what you specifically mean here? Time alignment between the drivers needs to be repeated? Can you describe exactly what filters you are applying?
As of now I assume you are doing the following.
Case 1 - Linear Phase LR4 50 Hz Crossover
-Apply linear phase LR4 LPF @ 50 Hz to sub
-Apply linear phase LR4 HPF @ 50 Hz to woofer
-Result is linear phase behavior
Case 2 - Minimum Phase LR4 50 Hz Crossover
-Apply minimum phase LR4 LPF @ 50 Hz to sub
-Apply minimum phase LR4 HPF @ 50 Hz to woofer
-Result is all-pass phase behavior, phase is 180 deg at 50 Hz
I don't see why any time alignment would be needed unless you are referring to adding global delay to case 2 to match the delay caused by the linear phase filter in case 1. There certainly shouldn't be any need to adjust the delay between the sub and woofer.
For reference, here are some electrical measurements of the above cases, all done at 48 kHz sample rate. Measurements are combined output. For case 1 I used 16384 tap FIR filters, for case 2 I used IIR. Source is TOSLINK output of a MacBook Pro. All processing done in CamillaDSP with a MOTU Ultralite Mk5, using digital input / output. REW capture device is a UR23 TOSLINK to USB card. Right channel is used as a loopback for timing reference. For reference here is the CamillaDSP pipeline of case 1.
First looking at magnitude response, as expected both are completely flat.
Next looking at phase response. Here I removed the 170.67 ms delay from case 1 which is caused by the FIR filter to eliminate unnecessary phase wraps. Clearly case 1 is linear phase, case 2 shows all pass behavior.
Next looking at impulse response for purposes of delay. Case 2 is delayed 170.67 ms due to the FIR filter latency compared to case 1.
If I add 170.67 ms delay to case 2 to match the delay of case 1 and re-meeasure, I get the following impulse response. Impulse peaks are exactly aligned.
Michael