I went through the update tonight. I'm using beta 11 but have been running manual updates against it so take my experience with a grain of salt.
I followed your instructions to update the scripts:
I ran into one problem running prog_refresh:
FINISHED copying bin files
FINISHED copying AX.25 files
/home/pi/bin/prog_refresh.sh: line 145: unexpected EOF while looking for matching `"'
/home/pi/bin/prog_refresh.sh: line 147: syntax error: unexpected end of file
This seemed curious as the file contains only 141 lines. I checked and it looks like right after finishing copying the AX25 files it updates the DRAWs manager. I've run it a second time after finishing all of this and it simply states that the DRAWs manager is up to date, and everything else appears to be in order
I then proceeded with hf_verchk.sh -u which installed the fldigi source and compiled it - that seemed to take close to 30 minutes on my 3b+.
After that i rebooted, checked my audio and re-ran "prog_refresh -c"
pi@n3ap-p:~/n7nix/hfprogs $ prog_refresh.sh -c
js8call: current version: 1.0.0, installed: 1.0.0
wsjtx: current version: 2.0.1, installed: 2.0.1
Library: libflxmlrpc IS loaded.
flxmlrpc: current version: 0.1.4, installed: 0.1.4
fldigi: current version: 4.1.02, installed: 4.1.02
flrig: current version: 1.3.43, installed: 1.3.43
flmsg: current version: 4.0.8, installed: 4.0.8
flamp: current version: 2.2.04, installed: 2.2.04
Source not downloaded.
xs_verchk.sh: Detected xastir package.
xastir: current version: , installed: 2.0.8?
gp_verchk.sh: Detected gpsd package.
gpsd: current version: 3.18.1, installed: 3.18.1
All looks good, i've been using js8 and fldigi tonight so far with no issues or changes in behavior.